rs11717948

Variant names:

• chr3-183591640-G-A
• rs11717948

Your query was ambiguous. Multiple possible variants found:

• chr3-183591640-G-A
• chr3-183591640-G-C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The variant allele was found at a frequency of 0.0287 in 152,178 control chromosomes in the GnomAD database, including 84 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 0.029 (84 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.235
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BS1: Variant frequency is greater than expected in population nfe. GnomAd4 allele frequency = 0.0287 (4371/152178) while in subpopulation NFE AF = 0.0392 (2663/67998). AF 95% confidence interval is 0.0379. There are 84 homozygotes in GnomAd4. There are 2029 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 84 gene

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: 0.0288 AC: 4376 AN: 152060 Hom.: 85 Cov.: 32

Gnomad AFR AF: 0.00845

Gnomad AMI AF: 0.0549

Gnomad AMR AF: 0.0340

Gnomad ASJ AF: 0.0903

Gnomad EAS AF: 0.000385

Gnomad SAS AF: 0.0216

Gnomad FIN AF: 0.0249

Gnomad MID AF: 0.0955

Gnomad NFE AF: 0.0392

Gnomad OTH AF: 0.0374

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

GnomAD4 genome AF: 0.0287 AC: 4371 AN: 152178 Hom.: 84 Cov.: 32 AF XY: 0.0273 AC XY: 2029 AN XY: 74390

African (AFR) AF: 0.00843 AC: 350 AN: 41532

American (AMR) AF: 0.0340 AC: 519 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.0903 AC: 313 AN: 3468

East Asian (EAS) AF: 0.000386 AC: 2 AN: 5182

South Asian (SAS) AF: 0.0214 AC: 103 AN: 4816

European-Finnish (FIN) AF: 0.0249 AC: 264 AN: 10588

Middle Eastern (MID) AF: 0.0993 AC: 29 AN: 292

European-Non Finnish (NFE) AF: 0.0392 AC: 2663 AN: 67998

Other (OTH) AF: 0.0370 AC: 78 AN: 2110

Alfa AF: 0.0258 Hom.: 27

Bravo AF: 0.0293

Asia WGS AF: 0.0110 AC: 37 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	4.3
DANN	Benign	0.81
PhyloP100		-0.23

Splicing

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

Other links and lift over

dbSNP: rs11717948; hg19: chr3-183309428;