rs3997854

Variant names:

• chr6-32715138-T-A
• rs3997854

Your query was ambiguous. Multiple possible variants found:

• chr6-32715138-T-A
• chr6-32715138-T-G

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 0.032 in 152,146 control chromosomes in the GnomAD database, including 128 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 0.032 (128 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.20
• Publications: 21 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 (SAS) allele frequency at 95% confidence interval = 0.0878 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: 0.0321 AC: 4875 AN: 152028 Hom.: 129 Cov.: 32

Gnomad AFR AF: 0.0412

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.0279

Gnomad ASJ AF: 0.0662

Gnomad EAS AF: 0.0459

Gnomad SAS AF: 0.0945

Gnomad FIN AF: 0.0221

Gnomad MID AF: 0.0791

Gnomad NFE AF: 0.0219

Gnomad OTH AF: 0.0335

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

GnomAD4 genome AF: 0.0320 AC: 4875 AN: 152146 Hom.: 128 Cov.: 32 AF XY: 0.0338 AC XY: 2516 AN XY: 74384

African (AFR) AF: 0.0411 AC: 1706 AN: 41490

American (AMR) AF: 0.0279 AC: 427 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0662 AC: 230 AN: 3472

East Asian (EAS) AF: 0.0460 AC: 238 AN: 5178

South Asian (SAS) AF: 0.0950 AC: 458 AN: 4820

European-Finnish (FIN) AF: 0.0221 AC: 234 AN: 10576

Middle Eastern (MID) AF: 0.0782 AC: 23 AN: 294

European-Non Finnish (NFE) AF: 0.0219 AC: 1488 AN: 67992

Other (OTH) AF: 0.0331 AC: 70 AN: 2114

Alfa AF: 0.00169 Hom.: 1299

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.12
DANN	Benign	0.21
PhyloP100		-3.2

Splicing

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

Other links and lift over

dbSNP: rs3997854; hg19: chr6-32682915;