rs9861643

Variant names:

• chr3-38655848-C-T
• rs9861643

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 0.232 in 152,186 control chromosomes in the GnomAD database, including 4,558 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 0.23 (4558 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.613
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.353 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: 0.231 AC: 35177 AN: 152068 Hom.: 4549 Cov.: 33

Gnomad AFR AF: 0.325

Gnomad AMI AF: 0.105

Gnomad AMR AF: 0.301

Gnomad ASJ AF: 0.125

Gnomad EAS AF: 0.367

Gnomad SAS AF: 0.0954

Gnomad FIN AF: 0.204

Gnomad MID AF: 0.231

Gnomad NFE AF: 0.169

Gnomad OTH AF: 0.228

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

GnomAD4 genome AF: 0.232 AC: 35233 AN: 152186 Hom.: 4558 Cov.: 33 AF XY: 0.234 AC XY: 17414 AN XY: 74400

African (AFR) AF: 0.325 AC: 13499 AN: 41498

American (AMR) AF: 0.301 AC: 4608 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.125 AC: 432 AN: 3466

East Asian (EAS) AF: 0.367 AC: 1900 AN: 5176

South Asian (SAS) AF: 0.0959 AC: 463 AN: 4828

European-Finnish (FIN) AF: 0.204 AC: 2164 AN: 10592

Middle Eastern (MID) AF: 0.248 AC: 73 AN: 294

European-Non Finnish (NFE) AF: 0.169 AC: 11520 AN: 68012

Other (OTH) AF: 0.226 AC: 478 AN: 2114

Alfa AF: 0.194 Hom.: 12140

Bravo AF: 0.246

Asia WGS AF: 0.223 AC: 773 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	6.3
DANN	Benign	0.66
PhyloP100		0.61

Splicing

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

Other links and lift over

dbSNP: rs9861643; hg19: chr3-38697339;