rs2109750

Variant names:

• chr14-74204553-G-A
• rs2109750

Your query was ambiguous. Multiple possible variants found:

• chr14-74204553-G-A
• chr14-74204553-G-C
• chr14-74204553-G-T

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 0.404 in 152,014 control chromosomes in the GnomAD database, including 13,444 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 0.40 (13444 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.175
• Publications: 9 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.483 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: 0.405 AC: 61443 AN: 151896 Hom.: 13435 Cov.: 32

Gnomad AFR AF: 0.294

Gnomad AMI AF: 0.296

Gnomad AMR AF: 0.416

Gnomad ASJ AF: 0.458

Gnomad EAS AF: 0.0595

Gnomad SAS AF: 0.283

Gnomad FIN AF: 0.504

Gnomad MID AF: 0.351

Gnomad NFE AF: 0.488

Gnomad OTH AF: 0.406

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

GnomAD4 genome AF: 0.404 AC: 61476 AN: 152014 Hom.: 13444 Cov.: 32 AF XY: 0.403 AC XY: 29953 AN XY: 74294

African (AFR) AF: 0.294 AC: 12191 AN: 41476

American (AMR) AF: 0.416 AC: 6354 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.458 AC: 1589 AN: 3470

East Asian (EAS) AF: 0.0592 AC: 306 AN: 5166

South Asian (SAS) AF: 0.283 AC: 1366 AN: 4820

European-Finnish (FIN) AF: 0.504 AC: 5314 AN: 10552

Middle Eastern (MID) AF: 0.340 AC: 100 AN: 294

European-Non Finnish (NFE) AF: 0.488 AC: 33125 AN: 67942

Other (OTH) AF: 0.409 AC: 862 AN: 2110

Alfa AF: 0.452 Hom.: 68048

Bravo AF: 0.390

Asia WGS AF: 0.233 AC: 812 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	2.2
DANN	Benign	0.30
PhyloP100		0.17

Splicing

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

Other links and lift over

dbSNP: rs2109750; hg19: chr14-74671256;