chr2-127610660-T-C

Variant names:

• chr2-127610660-T-C
• rs777433
• NM_001393586.1:c.3192+644T>C

Variant summary

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

The NM_001393586.1(MYO7B):​c.3192+644T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.344 in 152,240 control chromosomes in the GnomAD database, including 9,282 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 0.34 (9282 hom., cov: 34)
• Consequence: MYO7B NM_001393586.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.12
• Publications: 8 publications found

Genes affected

MYO7B (HGNC:7607): (myosin VIIB) The protein encoded by this gene is found in brush border microvilli of epithelial cells in the intestines and kidneys. The encoded protein is involved in linking protocadherins to the actin cytoskeleton and is essential for proper microvilli function. This protein aids in the accumulation of intermicrovillar adhesion components such as harmonin and ANKS4B, and this accumulation is necessary for normal brush border action. [provided by RefSeq, Jan 2017]

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 (SAS) allele frequency at 95% confidence interval = 0.371 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MYO7B	NM_001393586.1	c.3192+644T>C		intron_variant	Intron 24 of 47	ENST00000409816.8	NP_001380515.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MYO7B	ENST00000409816.8	c.3192+644T>C		intron_variant	Intron 24 of 47	1	NM_001393586.1	ENSP00000386461.3
MYO7B	ENST00000428314.5	c.3192+644T>C		intron_variant	Intron 24 of 46	5		ENSP00000415090.1

Frequencies

GnomAD3 genomes AF: 0.344 AC: 52314 AN: 152122 Hom.: 9269 Cov.: 34

Gnomad AFR AF: 0.351

Gnomad AMI AF: 0.145

Gnomad AMR AF: 0.279

Gnomad ASJ AF: 0.360

Gnomad EAS AF: 0.127

Gnomad SAS AF: 0.389

Gnomad FIN AF: 0.389

Gnomad MID AF: 0.383

Gnomad NFE AF: 0.362

Gnomad OTH AF: 0.372

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

GnomAD4 genome AF: 0.344 AC: 52359 AN: 152240 Hom.: 9282 Cov.: 34 AF XY: 0.343 AC XY: 25528 AN XY: 74436

African (AFR) AF: 0.351 AC: 14584 AN: 41550

American (AMR) AF: 0.279 AC: 4263 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.360 AC: 1250 AN: 3472

East Asian (EAS) AF: 0.127 AC: 658 AN: 5192

South Asian (SAS) AF: 0.386 AC: 1864 AN: 4828

European-Finnish (FIN) AF: 0.389 AC: 4125 AN: 10602

Middle Eastern (MID) AF: 0.364 AC: 107 AN: 294

European-Non Finnish (NFE) AF: 0.362 AC: 24579 AN: 67978

Other (OTH) AF: 0.377 AC: 797 AN: 2114

Alfa AF: 0.354 Hom.: 39642

Bravo AF: 0.330

Asia WGS AF: 0.322 AC: 1121 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.77
DANN	Benign	0.46
PhyloP100		-1.1
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: rs777433; hg19: chr2-128368235;