rs2069614

Variant names:

• chr5-132071908-T-C
• rs2069614

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 0.401 in 152,032 control chromosomes in the GnomAD database, including 13,069 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 (13069 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.13
• Publications: 16 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.489 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: 0.401 AC: 60857 AN: 151914 Hom.: 13054 Cov.: 32

Gnomad AFR AF: 0.495

Gnomad AMI AF: 0.592

Gnomad AMR AF: 0.346

Gnomad ASJ AF: 0.341

Gnomad EAS AF: 0.00328

Gnomad SAS AF: 0.128

Gnomad FIN AF: 0.271

Gnomad MID AF: 0.310

Gnomad NFE AF: 0.426

Gnomad OTH AF: 0.412

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

GnomAD4 genome AF: 0.401 AC: 60896 AN: 152032 Hom.: 13069 Cov.: 32 AF XY: 0.384 AC XY: 28525 AN XY: 74316

African (AFR) AF: 0.495 AC: 20520 AN: 41460

American (AMR) AF: 0.345 AC: 5274 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.341 AC: 1182 AN: 3470

East Asian (EAS) AF: 0.00328 AC: 17 AN: 5176

South Asian (SAS) AF: 0.128 AC: 614 AN: 4810

European-Finnish (FIN) AF: 0.271 AC: 2865 AN: 10566

Middle Eastern (MID) AF: 0.313 AC: 92 AN: 294

European-Non Finnish (NFE) AF: 0.426 AC: 28934 AN: 67964

Other (OTH) AF: 0.407 AC: 859 AN: 2112

Alfa AF: 0.416 Hom.: 2153

Bravo AF: 0.415

Asia WGS AF: 0.0880 AC: 307 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.089
DANN	Benign	0.58
PhyloP100		-2.1

Splicing

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

Other links and lift over

dbSNP: rs2069614; hg19: chr5-131407601; COSMIC: COSV51522278;