rs3997872

Variant names:

• chr6-32612840-T-A
• rs3997872

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 0.139 in 152,224 control chromosomes in the GnomAD database, including 1,676 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 0.14 (1676 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.491
• Publications: 31 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.195 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: 0.139 AC: 21133 AN: 152106 Hom.: 1674 Cov.: 33

Gnomad AFR AF: 0.0897

Gnomad AMI AF: 0.159

Gnomad AMR AF: 0.200

Gnomad ASJ AF: 0.190

Gnomad EAS AF: 0.0777

Gnomad SAS AF: 0.0730

Gnomad FIN AF: 0.141

Gnomad MID AF: 0.114

Gnomad NFE AF: 0.162

Gnomad OTH AF: 0.126

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

GnomAD4 genome AF: 0.139 AC: 21158 AN: 152224 Hom.: 1676 Cov.: 33 AF XY: 0.138 AC XY: 10235 AN XY: 74426

African (AFR) AF: 0.0898 AC: 3733 AN: 41548

American (AMR) AF: 0.201 AC: 3069 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.190 AC: 660 AN: 3468

East Asian (EAS) AF: 0.0781 AC: 405 AN: 5188

South Asian (SAS) AF: 0.0731 AC: 353 AN: 4830

European-Finnish (FIN) AF: 0.141 AC: 1498 AN: 10588

Middle Eastern (MID) AF: 0.116 AC: 34 AN: 294

European-Non Finnish (NFE) AF: 0.162 AC: 10998 AN: 68008

Other (OTH) AF: 0.125 AC: 263 AN: 2104

Alfa AF: 0.146 Hom.: 224

Bravo AF: 0.147

Asia WGS AF: 0.0770 AC: 271 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	5.2
DANN	Benign	0.82
PhyloP100		-0.49

Splicing

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

Other links and lift over

dbSNP: rs3997872; hg19: chr6-32580617;