chr2-14661377-G-A

Variant names:

• chr2-14661377-G-A
• rs7602441

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 0.268 in 152,062 control chromosomes in the GnomAD database, including 8,744 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 0.27 (8744 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.13
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.59 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.268 AC: 40720 AN: 151944 Hom.: 8708 Cov.: 33

Gnomad AFR AF: 0.596

Gnomad AMI AF: 0.123

Gnomad AMR AF: 0.208

Gnomad ASJ AF: 0.0955

Gnomad EAS AF: 0.235

Gnomad SAS AF: 0.127

Gnomad FIN AF: 0.146

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.126

Gnomad OTH AF: 0.221

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

GnomAD4 genome AF: 0.268 AC: 40813 AN: 152062 Hom.: 8744 Cov.: 33 AF XY: 0.265 AC XY: 19667 AN XY: 74352

African (AFR) AF: 0.596 AC: 24709 AN: 41452

American (AMR) AF: 0.208 AC: 3175 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.0955 AC: 331 AN: 3466

East Asian (EAS) AF: 0.235 AC: 1214 AN: 5160

South Asian (SAS) AF: 0.126 AC: 606 AN: 4826

European-Finnish (FIN) AF: 0.146 AC: 1546 AN: 10594

Middle Eastern (MID) AF: 0.150 AC: 44 AN: 294

European-Non Finnish (NFE) AF: 0.126 AC: 8594 AN: 67968

Other (OTH) AF: 0.228 AC: 482 AN: 2114

Alfa AF: 0.176 Hom.: 10205

Bravo AF: 0.290

Asia WGS AF: 0.190 AC: 660 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.23
DANN	Benign	0.40
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs7602441; hg19: chr2-14801501;