rs12948385

Variant names:

• chr17-1761607-G-A
• rs12948385

Your query was ambiguous. Multiple possible variants found:

• chr17-1761607-G-A
• chr17-1761607-G-C

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 0.263 in 152,040 control chromosomes in the GnomAD database, including 6,606 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 0.26 (6606 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.198
• Publications: 21 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.367 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.263 AC: 40005 AN: 151922 Hom.: 6610 Cov.: 32

Gnomad AFR AF: 0.0736

Gnomad AMI AF: 0.530

Gnomad AMR AF: 0.228

Gnomad ASJ AF: 0.347

Gnomad EAS AF: 0.276

Gnomad SAS AF: 0.241

Gnomad FIN AF: 0.311

Gnomad MID AF: 0.367

Gnomad NFE AF: 0.371

Gnomad OTH AF: 0.289

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

GnomAD4 genome AF: 0.263 AC: 39994 AN: 152040 Hom.: 6606 Cov.: 32 AF XY: 0.261 AC XY: 19406 AN XY: 74306

African (AFR) AF: 0.0734 AC: 3047 AN: 41496

American (AMR) AF: 0.228 AC: 3474 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.347 AC: 1204 AN: 3466

East Asian (EAS) AF: 0.275 AC: 1421 AN: 5160

South Asian (SAS) AF: 0.241 AC: 1161 AN: 4812

European-Finnish (FIN) AF: 0.311 AC: 3285 AN: 10574

Middle Eastern (MID) AF: 0.367 AC: 108 AN: 294

European-Non Finnish (NFE) AF: 0.371 AC: 25209 AN: 67954

Other (OTH) AF: 0.286 AC: 604 AN: 2110

Alfa AF: 0.285 Hom.: 981

Bravo AF: 0.250

Asia WGS AF: 0.205 AC: 715 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.8
DANN	Benign	0.86
PhyloP100		0.20
PromoterAI		0.0069	Neutral

Splicing

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

Other links and lift over

dbSNP: rs12948385; hg19: chr17-1664901;