6-126645162-T-C

Position:

• chr6-126645162-T-C

Variant summary

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

The ENST00000651326.1(ENSG00000293110):​n.694-41697A>G 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 0.49 in 151,976 control chromosomes in the GnomAD database, including 19,725 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 0.49 (19725 hom., cov: 32)
• Consequence: ENST00000651326.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.926

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.953 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
	ENST00000651326.1	n.694-41697A>G		intron_variant, non_coding_transcript_variant
	ENST00000650727.1	n.1167-23289A>G		intron_variant, non_coding_transcript_variant
	ENST00000652545.1	n.1477-23289A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.490 AC: 74450 AN: 151858 Hom.: 19716 Cov.: 32

Gnomad AFR AF: 0.341

Gnomad AMI AF: 0.486

Gnomad AMR AF: 0.639

Gnomad ASJ AF: 0.550

Gnomad EAS AF: 0.975

Gnomad SAS AF: 0.705

Gnomad FIN AF: 0.474

Gnomad MID AF: 0.618

Gnomad NFE AF: 0.493

Gnomad OTH AF: 0.516

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

GnomAD4 genome AF: 0.490 AC: 74487 AN: 151976 Hom.: 19725 Cov.: 32 AF XY: 0.500 AC XY: 37132 AN XY: 74288

Gnomad4 AFR AF: 0.341

Gnomad4 AMR AF: 0.640

Gnomad4 ASJ AF: 0.550

Gnomad4 EAS AF: 0.975

Gnomad4 SAS AF: 0.706

Gnomad4 FIN AF: 0.474

Gnomad4 NFE AF: 0.493

Gnomad4 OTH AF: 0.513

Alfa AF: 0.514 Hom.: 29774

Bravo AF: 0.499

Asia WGS AF: 0.718 AC: 2489 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.3
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: rs4549631; hg19: chr6-126966308; COSMIC: COSV69095955;