6-126645162-T-C

Variant names:

• chr6-126645162-T-C
• rs4549631
• ENST00000650727.1:n.1167-23289A>G

Variant summary

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

The ENST00000650727.1(ENSG00000286215):​n.1167-23289A>G variant causes a intron 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: ENSG00000286215 ENST00000650727.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.926

Genes affected

ENSG00000286215 (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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000286215	ENST00000650727.1	n.1167-23289A>G		intron_variant	Intron 9 of 14
ENSG00000286215	ENST00000651326.1	n.694-41697A>G		intron_variant	Intron 3 of 6
ENSG00000286215	ENST00000652545.1	n.1477-23289A>G		intron_variant	Intron 10 of 15

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;