rs3997849

Variant names:

• chr6-32714625-C-T
• rs3997849

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 0.288 in 151,970 control chromosomes in the GnomAD database, including 6,738 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 0.29 (6738 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.124
• Publications: 18 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.409 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: 0.288 AC: 43806 AN: 151852 Hom.: 6742 Cov.: 33

Gnomad AFR AF: 0.211

Gnomad AMI AF: 0.171

Gnomad AMR AF: 0.265

Gnomad ASJ AF: 0.441

Gnomad EAS AF: 0.204

Gnomad SAS AF: 0.427

Gnomad FIN AF: 0.241

Gnomad MID AF: 0.405

Gnomad NFE AF: 0.337

Gnomad OTH AF: 0.327

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

GnomAD4 genome AF: 0.288 AC: 43808 AN: 151970 Hom.: 6738 Cov.: 33 AF XY: 0.285 AC XY: 21189 AN XY: 74280

African (AFR) AF: 0.210 AC: 8721 AN: 41444

American (AMR) AF: 0.264 AC: 4035 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.441 AC: 1528 AN: 3464

East Asian (EAS) AF: 0.205 AC: 1062 AN: 5186

South Asian (SAS) AF: 0.425 AC: 2041 AN: 4808

European-Finnish (FIN) AF: 0.241 AC: 2540 AN: 10532

Middle Eastern (MID) AF: 0.391 AC: 115 AN: 294

European-Non Finnish (NFE) AF: 0.337 AC: 22913 AN: 67952

Other (OTH) AF: 0.330 AC: 698 AN: 2114

Alfa AF: 0.314 Hom.: 16509

Bravo AF: 0.284

Asia WGS AF: 0.325 AC: 1127 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	6.6
DANN	Benign	0.53
PhyloP100		0.12

Splicing

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

Other links and lift over

dbSNP: rs3997849; hg19: chr6-32682402;