rs679582

Positions:

• chr6-139510043-G-A

Variant summary

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

The ENST00000647815.1(ENSG00000226571):​n.134+23428G>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 0.56 in 151,954 control chromosomes in the GnomAD database, including 24,406 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 0.56 (24406 hom., cov: 32)
• Consequence: ENST00000647815.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.784

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.693 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000647815.1	n.134+23428G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.560 AC: 84984 AN: 151836 Hom.: 24384 Cov.: 32

Gnomad AFR AF: 0.453

Gnomad AMI AF: 0.652

Gnomad AMR AF: 0.581

Gnomad ASJ AF: 0.661

Gnomad EAS AF: 0.307

Gnomad SAS AF: 0.711

Gnomad FIN AF: 0.547

Gnomad MID AF: 0.573

Gnomad NFE AF: 0.623

Gnomad OTH AF: 0.583

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

GnomAD4 genome AF: 0.560 AC: 85053 AN: 151954 Hom.: 24406 Cov.: 32 AF XY: 0.560 AC XY: 41563 AN XY: 74280

Gnomad4 AFR AF: 0.453

Gnomad4 AMR AF: 0.582

Gnomad4 ASJ AF: 0.661

Gnomad4 EAS AF: 0.307

Gnomad4 SAS AF: 0.713

Gnomad4 FIN AF: 0.547

Gnomad4 NFE AF: 0.623

Gnomad4 OTH AF: 0.578

Alfa AF: 0.585 Hom.: 3521

Bravo AF: 0.552

Asia WGS AF: 0.533 AC: 1853 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.12
DANN	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs679582; hg19: chr6-139831180; COSMIC: COSV69428605;