rs628751

chr6-139517282-C-A

Variant summary

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

The ENST00000647815.1(ENSG00000226571):n.134+30667C>A 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 0.411 in 151,944 control chromosomes in the GnomAD database, including 14,785 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 0.41 (14785 hom., cov: 32)
• Consequence: ENST00000647815.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.24

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.634 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000647815.1	n.134+30667C>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.411 AC: 62464 AN: 151828 Hom.: 14771 Cov.: 32

Gnomad AFR AF: 0.168

Gnomad AMI AF: 0.560

Gnomad AMR AF: 0.483

Gnomad ASJ AF: 0.537

Gnomad EAS AF: 0.271

Gnomad SAS AF: 0.651

Gnomad FIN AF: 0.453

Gnomad MID AF: 0.478

Gnomad NFE AF: 0.521

Gnomad OTH AF: 0.435

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

GnomAD4 genome AF: 0.411 AC: 62488 AN: 151944 Hom.: 14785 Cov.: 32 AF XY: 0.413 AC XY: 30659 AN XY: 74250

Gnomad4 AFR AF: 0.168

Gnomad4 AMR AF: 0.484

Gnomad4 ASJ AF: 0.537

Gnomad4 EAS AF: 0.271

Gnomad4 SAS AF: 0.653

Gnomad4 FIN AF: 0.453

Gnomad4 NFE AF: 0.521

Gnomad4 OTH AF: 0.432

Alfa AF: 0.471 Hom.: 7010

Bravo AF: 0.396

Asia WGS AF: 0.469 AC: 1628 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
Cadd	Benign	1.0
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: rs628751; hg19: chr6-139838419; COSMIC: COSV69428627;