rs6503319

chr17-10670842-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XM_011523870.4(MYH3):c.-68+7428G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.31 in 151,948 control chromosomes in the GnomAD database, including 7,992 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 0.31 (7992 hom., cov: 32)
• Consequence: MYH3 XM_011523870.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.61

Genes affected

MYH3 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.441 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MYH3	XM_011523870.4	c.-68+7428G>A		intron_variant
MYH3	XM_047436127.1	c.-3163-2108G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.309 AC: 46976 AN: 151830 Hom.: 7963 Cov.: 32

Gnomad AFR AF: 0.446

Gnomad AMI AF: 0.296

Gnomad AMR AF: 0.212

Gnomad ASJ AF: 0.254

Gnomad EAS AF: 0.381

Gnomad SAS AF: 0.352

Gnomad FIN AF: 0.200

Gnomad MID AF: 0.277

Gnomad NFE AF: 0.260

Gnomad OTH AF: 0.306

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

GnomAD4 genome AF: 0.310 AC: 47053 AN: 151948 Hom.: 7992 Cov.: 32 AF XY: 0.306 AC XY: 22753 AN XY: 74268

Gnomad4 AFR AF: 0.447

Gnomad4 AMR AF: 0.211

Gnomad4 ASJ AF: 0.254

Gnomad4 EAS AF: 0.380

Gnomad4 SAS AF: 0.352

Gnomad4 FIN AF: 0.200

Gnomad4 NFE AF: 0.260

Gnomad4 OTH AF: 0.312

Alfa AF: 0.269 Hom.: 10373

Bravo AF: 0.316

Asia WGS AF: 0.362 AC: 1260 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
Cadd	Benign	0.046
Dann	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6503319; hg19: chr17-10574159;