chr6-31142105-G-T

Variant names:

• chr6-31142105-G-T
• rs1265086

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.432 in 151,080 control chromosomes in the GnomAD database, including 14,502 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 0.43 (14502 hom., cov: 28)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.792
• Publications: 27 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.503 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

Frequencies

GnomAD3 genomes AF: 0.432 AC: 65260 AN: 150964 Hom.: 14477 Cov.: 28

Gnomad AFR AF: 0.508

Gnomad AMI AF: 0.529

Gnomad AMR AF: 0.414

Gnomad ASJ AF: 0.549

Gnomad EAS AF: 0.358

Gnomad SAS AF: 0.430

Gnomad FIN AF: 0.413

Gnomad MID AF: 0.579

Gnomad NFE AF: 0.389

Gnomad OTH AF: 0.500

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

GnomAD4 genome AF: 0.432 AC: 65330 AN: 151080 Hom.: 14502 Cov.: 28 AF XY: 0.435 AC XY: 32100 AN XY: 73782

African (AFR) AF: 0.509 AC: 20975 AN: 41242

American (AMR) AF: 0.413 AC: 6273 AN: 15180

Ashkenazi Jewish (ASJ) AF: 0.549 AC: 1903 AN: 3464

East Asian (EAS) AF: 0.358 AC: 1839 AN: 5138

South Asian (SAS) AF: 0.431 AC: 2068 AN: 4796

European-Finnish (FIN) AF: 0.413 AC: 4305 AN: 10414

Middle Eastern (MID) AF: 0.575 AC: 169 AN: 294

European-Non Finnish (NFE) AF: 0.389 AC: 26285 AN: 67562

Other (OTH) AF: 0.496 AC: 1036 AN: 2088

Alfa AF: 0.505 Hom.: 77927

Bravo AF: 0.506

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.49
DANN	Benign	0.78
PhyloP100		-0.79

Splicing

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

Other links and lift over

dbSNP: rs1265086; hg19: chr6-31109882;