rs11654423

chr17-10442014-C-T

Variant summary

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

The NR_125367.1(MYHAS):n.167+35776C>T variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.32 in 151,950 control chromosomes in the GnomAD database, including 8,938 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 0.32 (8938 hom., cov: 32)
• Consequence: MYHAS NR_125367.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.118

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.795 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MYHAS	NR_125367.1	n.167+35776C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000399342.6	n.206+35737C>T		intron_variant, non_coding_transcript_variant		3
	ENST00000581304.1	n.143+35776C>T		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.320 AC: 48659 AN: 151832 Hom.: 8941 Cov.: 32

Gnomad AFR AF: 0.221

Gnomad AMI AF: 0.353

Gnomad AMR AF: 0.412

Gnomad ASJ AF: 0.318

Gnomad EAS AF: 0.816

Gnomad SAS AF: 0.487

Gnomad FIN AF: 0.383

Gnomad MID AF: 0.335

Gnomad NFE AF: 0.302

Gnomad OTH AF: 0.297

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

GnomAD4 genome AF: 0.320 AC: 48679 AN: 151950 Hom.: 8938 Cov.: 32 AF XY: 0.333 AC XY: 24729 AN XY: 74254

Gnomad4 AFR AF: 0.221

Gnomad4 AMR AF: 0.412

Gnomad4 ASJ AF: 0.318

Gnomad4 EAS AF: 0.816

Gnomad4 SAS AF: 0.486

Gnomad4 FIN AF: 0.383

Gnomad4 NFE AF: 0.302

Gnomad4 OTH AF: 0.298

Alfa AF: 0.302 Hom.: 5880

Bravo AF: 0.317

Asia WGS AF: 0.580 AC: 2010 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
Cadd	Benign	5.0
Dann	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11654423; hg19: chr17-10345331;