6-31597044-C-T

Variant names:

• chr6-31597044-C-T
• rs2844480

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 0.172 in 152,064 control chromosomes in the GnomAD database, including 2,358 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 0.17 (2358 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.268
• Publications: 37 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.75).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.288 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: 0.172 AC: 26118 AN: 151946 Hom.: 2360 Cov.: 31

Gnomad AFR AF: 0.127

Gnomad AMI AF: 0.182

Gnomad AMR AF: 0.147

Gnomad ASJ AF: 0.189

Gnomad EAS AF: 0.127

Gnomad SAS AF: 0.303

Gnomad FIN AF: 0.173

Gnomad MID AF: 0.165

Gnomad NFE AF: 0.197

Gnomad OTH AF: 0.191

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

GnomAD4 genome AF: 0.172 AC: 26131 AN: 152064 Hom.: 2358 Cov.: 31 AF XY: 0.173 AC XY: 12835 AN XY: 74340

African (AFR) AF: 0.127 AC: 5272 AN: 41492

American (AMR) AF: 0.147 AC: 2241 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.189 AC: 656 AN: 3470

East Asian (EAS) AF: 0.128 AC: 661 AN: 5182

South Asian (SAS) AF: 0.301 AC: 1451 AN: 4820

European-Finnish (FIN) AF: 0.173 AC: 1826 AN: 10578

Middle Eastern (MID) AF: 0.170 AC: 50 AN: 294

European-Non Finnish (NFE) AF: 0.197 AC: 13406 AN: 67964

Other (OTH) AF: 0.191 AC: 402 AN: 2104

Alfa AF: 0.191 Hom.: 11983

Bravo AF: 0.167

Asia WGS AF: 0.231 AC: 802 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	2.3
DANN	Benign	0.86
PhyloP100		0.27

Splicing

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

Other links and lift over

dbSNP: rs2844480; hg19: chr6-31564821;