2-14661789-G-A

Variant names:

• chr2-14661789-G-A
• rs7602960

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 0.513 in 151,536 control chromosomes in the GnomAD database, including 23,235 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 0.51 (23235 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.129
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.66).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.841 is higher than 0.05.

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: 0.513 AC: 77620 AN: 151418 Hom.: 23178 Cov.: 30

Gnomad AFR AF: 0.848

Gnomad AMI AF: 0.284

Gnomad AMR AF: 0.439

Gnomad ASJ AF: 0.349

Gnomad EAS AF: 0.351

Gnomad SAS AF: 0.405

Gnomad FIN AF: 0.396

Gnomad MID AF: 0.408

Gnomad NFE AF: 0.376

Gnomad OTH AF: 0.475

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

GnomAD4 genome AF: 0.513 AC: 77743 AN: 151536 Hom.: 23235 Cov.: 30 AF XY: 0.511 AC XY: 37824 AN XY: 74002

African (AFR) AF: 0.848 AC: 35077 AN: 41356

American (AMR) AF: 0.439 AC: 6666 AN: 15178

Ashkenazi Jewish (ASJ) AF: 0.349 AC: 1208 AN: 3458

East Asian (EAS) AF: 0.352 AC: 1807 AN: 5140

South Asian (SAS) AF: 0.404 AC: 1927 AN: 4772

European-Finnish (FIN) AF: 0.396 AC: 4154 AN: 10490

Middle Eastern (MID) AF: 0.418 AC: 122 AN: 292

European-Non Finnish (NFE) AF: 0.376 AC: 25526 AN: 67852

Other (OTH) AF: 0.478 AC: 998 AN: 2088

Alfa AF: 0.260 Hom.: 519

Bravo AF: 0.536

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.66
CADD	Benign	2.8
DANN	Benign	0.68
PhyloP100		-0.13

Splicing

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

Other links and lift over

dbSNP: rs7602960; hg19: chr2-14801913;