chr3-40008784-G-A

Variant names:

• chr3-40008784-G-A
• rs6791790
• NM_015460.4:c.111-35266G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_015460.4(MYRIP):​c.111-35266G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.101 in 152,234 control chromosomes in the GnomAD database, including 1,358 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.10 (1358 hom., cov: 32)
• Consequence: MYRIP NM_015460.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.563
• Publications: 2 publications found

Genes affected

MYRIP (HGNC:19156): (myosin VIIA and Rab interacting protein) Predicted to enable actin binding activity and myosin binding activity. Predicted to be involved in positive regulation of insulin secretion. Predicted to be located in actin cytoskeleton; dense core granule; and perinuclear region of cytoplasm. Predicted to be part of exocyst. Predicted to be active in cortical actin cytoskeleton. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.225 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_015460.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MYRIP	NM_015460.4	MANE Select	c.111-35266G>A		intron	N/A	NP_056275.2
	MYRIP	NM_001284423.2		c.111-35266G>A		intron	N/A	NP_001271352.1
	MYRIP	NM_001284424.2		c.111-35266G>A		intron	N/A	NP_001271353.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MYRIP	ENST00000302541.11	TSL:1 MANE Select	c.111-35266G>A		intron	N/A	ENSP00000301972.6
	MYRIP	ENST00000444716.5	TSL:1	c.111-35266G>A		intron	N/A	ENSP00000398665.1
	MYRIP	ENST00000396217.7	TSL:1	c.-20-35266G>A		intron	N/A	ENSP00000379519.3

Frequencies

GnomAD3 genomes AF: 0.101 AC: 15306 AN: 152116 Hom.: 1337 Cov.: 32

Gnomad AFR AF: 0.228

Gnomad AMI AF: 0.0208

Gnomad AMR AF: 0.0545

Gnomad ASJ AF: 0.0536

Gnomad EAS AF: 0.172

Gnomad SAS AF: 0.0491

Gnomad FIN AF: 0.0612

Gnomad MID AF: 0.0918

Gnomad NFE AF: 0.0414

Gnomad OTH AF: 0.0956

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.101 AC: 15385 AN: 152234 Hom.: 1358 Cov.: 32 AF XY: 0.100 AC XY: 7442 AN XY: 74424

African (AFR) AF: 0.229 AC: 9516 AN: 41506

American (AMR) AF: 0.0545 AC: 833 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0536 AC: 186 AN: 3468

East Asian (EAS) AF: 0.173 AC: 898 AN: 5182

South Asian (SAS) AF: 0.0487 AC: 235 AN: 4824

European-Finnish (FIN) AF: 0.0612 AC: 650 AN: 10614

Middle Eastern (MID) AF: 0.0850 AC: 25 AN: 294

European-Non Finnish (NFE) AF: 0.0414 AC: 2819 AN: 68024

Other (OTH) AF: 0.0965 AC: 204 AN: 2114

Alfa AF: 0.0613 Hom.: 2060

Bravo AF: 0.109

Asia WGS AF: 0.117 AC: 407 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.11
DANN	Benign	0.70
PhyloP100		-0.56
Mutation Taster		=100/0	polymorphism (auto)

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: rs6791790; hg19: chr3-40050275;