chr4-31736006-T-G

Variant names:

• chr4-31736006-T-G
• rs6846311

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 0.0744 in 152,126 control chromosomes in the GnomAD database, including 1,204 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 0.074 (1204 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0770
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.231 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: 0.0744 AC: 11315 AN: 152008 Hom.: 1208 Cov.: 32

Gnomad AFR AF: 0.235

Gnomad AMI AF: 0.0351

Gnomad AMR AF: 0.0283

Gnomad ASJ AF: 0.0213

Gnomad EAS AF: 0.000385

Gnomad SAS AF: 0.0151

Gnomad FIN AF: 0.00406

Gnomad MID AF: 0.00949

Gnomad NFE AF: 0.0117

Gnomad OTH AF: 0.0607

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

GnomAD4 genome AF: 0.0744 AC: 11324 AN: 152126 Hom.: 1204 Cov.: 32 AF XY: 0.0709 AC XY: 5277 AN XY: 74386

African (AFR) AF: 0.235 AC: 9743 AN: 41472

American (AMR) AF: 0.0283 AC: 432 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.0213 AC: 74 AN: 3470

East Asian (EAS) AF: 0.000386 AC: 2 AN: 5184

South Asian (SAS) AF: 0.0154 AC: 74 AN: 4820

European-Finnish (FIN) AF: 0.00406 AC: 43 AN: 10602

Middle Eastern (MID) AF: 0.00680 AC: 2 AN: 294

European-Non Finnish (NFE) AF: 0.0117 AC: 795 AN: 67972

Other (OTH) AF: 0.0601 AC: 127 AN: 2114

Alfa AF: 0.0389 Hom.: 163

Bravo AF: 0.0838

Asia WGS AF: 0.0220 AC: 75 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	3.5
DANN	Benign	0.46
PhyloP100		0.077

Splicing

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

Other links and lift over

dbSNP: rs6846311; hg19: chr4-31737628;