17-10384506-C-T

Position:

• chr17-10384506-C-T

Variant summary

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

The ENST00000399342.6(ENSG00000272736):​n.76+1299C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.446 in 151,958 control chromosomes in the GnomAD database, including 15,813 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 0.45 (15813 hom., cov: 31)
• Consequence: ENSG00000272736 ENST00000399342.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0660

Genes affected

ENSG00000272736 (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 (NFE) allele frequency at 95% confidence interval = 0.524 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MYHAS	NR_125367.1	n.76+1299C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000272736	ENST00000399342.6	n.76+1299C>T		intron_variant		3
ENSG00000272736	ENST00000581304.1	n.52+1299C>T		intron_variant		3
MYHAS	ENST00000587182.2	n.64+1299C>T		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.446 AC: 67722 AN: 151840 Hom.: 15808 Cov.: 31

Gnomad AFR AF: 0.367

Gnomad AMI AF: 0.384

Gnomad AMR AF: 0.415

Gnomad ASJ AF: 0.468

Gnomad EAS AF: 0.143

Gnomad SAS AF: 0.255

Gnomad FIN AF: 0.500

Gnomad MID AF: 0.383

Gnomad NFE AF: 0.529

Gnomad OTH AF: 0.459

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

GnomAD4 genome AF: 0.446 AC: 67763 AN: 151958 Hom.: 15813 Cov.: 31 AF XY: 0.436 AC XY: 32392 AN XY: 74250

Gnomad4 AFR AF: 0.367

Gnomad4 AMR AF: 0.414

Gnomad4 ASJ AF: 0.468

Gnomad4 EAS AF: 0.143

Gnomad4 SAS AF: 0.254

Gnomad4 FIN AF: 0.500

Gnomad4 NFE AF: 0.529

Gnomad4 OTH AF: 0.461

Alfa AF: 0.391 Hom.: 1688

Bravo AF: 0.440

Asia WGS AF: 0.242 AC: 847 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	6.2
DANN	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9906430; hg19: chr17-10287823;