rs820152

Variant names:

• chr17-75620008-T-A
• rs820152
• NM_001395058.1:c.7431T>A

Your query was ambiguous. Multiple possible variants found:

• chr17-75620008-T-A
• chr17-75620008-T-C
• chr17-75620008-T-G

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_001395058.1(MYO15B):​c.7431T>A​(p.Asn2477Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000658 in 152,086 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 8/10 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.0000066 (0 hom., cov: 34)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: MYO15B NM_001395058.1 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.706
• Publications: 19 publications found

Genes affected

MYO15B (HGNC:14083): (myosin XVB) Predicted to enable ATP binding activity; actin binding activity; and cytoskeletal motor activity. Predicted to be located in brush border; cytoplasm; and cytoskeleton. Predicted to be part of myosin complex. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.10399124).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001395058.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MYO15B	NM_001395058.1	MANE Select	c.7431T>A	p.Asn2477Lys	missense	Exon 47 of 64	NP_001381987.1
	MYO15B	NM_001309242.2		c.7317T>A	p.Asn2439Lys	missense	Exon 46 of 63	NP_001296171.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MYO15B	ENST00000645453.3	MANE Select	c.7431T>A	p.Asn2477Lys	missense	Exon 47 of 64	ENSP00000495242.3
	MYO15B	ENST00000642007.2		c.2988T>A	p.Asn996Lys	missense	Exon 26 of 42	ENSP00000492911.2
	MYO15B	ENST00000583140.5	TSL:2	c.129T>A	p.Asn43Lys	missense	Exon 1 of 3	ENSP00000488354.1

Frequencies

GnomAD3 genomes AF: 0.00000658 AC: 1 AN: 152086 Hom.: 0 Cov.: 34

Gnomad AFR AF: 0.0000241

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00

Gnomad OTH AF: 0.00

GnomAD4 exome Data not reliable, filtered out with message: AC0;AS_VQSR AF: 0.00 AC: 0 AN: 549408 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 297394

African (AFR) AF: 0.00 AC: 0 AN: 15796

American (AMR) AF: 0.00 AC: 0 AN: 34602

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 19908

East Asian (EAS) AF: 0.00 AC: 0 AN: 32094

South Asian (SAS) AF: 0.00 AC: 0 AN: 62570

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 33512

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 4066

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 316308

Other (OTH) AF: 0.00 AC: 0 AN: 30552

GnomAD4 genome AF: 0.00000658 AC: 1 AN: 152086 Hom.: 0 Cov.: 34 AF XY: 0.00 AC XY: 0 AN XY: 74272

African (AFR) AF: 0.0000241 AC: 1 AN: 41426

American (AMR) AF: 0.00 AC: 0 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3472

East Asian (EAS) AF: 0.00 AC: 0 AN: 5180

South Asian (SAS) AF: 0.00 AC: 0 AN: 4832

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10582

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 316

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 67988

Other (OTH) AF: 0.00 AC: 0 AN: 2092

Alfa AF: 0.00 Hom.: 9783

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.089
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.66
DANN	Benign	0.68
DEOGEN2	Benign	0.0082	T
FATHMM_MKL	Benign	0.077	N
LIST_S2	Benign	0.46	T
MetaRNN	Benign	0.10	T
PhyloP100		-0.71
Sift4G	Benign	0.070	T
Vest4		0.12
GERP RS		-7.4
PromoterAI		0.0034	Neutral
Varity_R		0.079

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs820152; hg19: chr17-73616088;