chr2-120437605-A-G

Variant names:

• chr2-120437605-A-G
• rs7581710

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 0.16 in 152,070 control chromosomes in the GnomAD database, including 2,777 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 0.16 (2777 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.97
• Publications: 11 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.307 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: 0.159 AC: 24209 AN: 151952 Hom.: 2767 Cov.: 32

Gnomad AFR AF: 0.311

Gnomad AMI AF: 0.0406

Gnomad AMR AF: 0.112

Gnomad ASJ AF: 0.122

Gnomad EAS AF: 0.197

Gnomad SAS AF: 0.294

Gnomad FIN AF: 0.0413

Gnomad MID AF: 0.133

Gnomad NFE AF: 0.0880

Gnomad OTH AF: 0.146

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

GnomAD4 genome AF: 0.160 AC: 24257 AN: 152070 Hom.: 2777 Cov.: 32 AF XY: 0.159 AC XY: 11801 AN XY: 74352

African (AFR) AF: 0.311 AC: 12896 AN: 41424

American (AMR) AF: 0.111 AC: 1700 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.122 AC: 425 AN: 3470

East Asian (EAS) AF: 0.197 AC: 1018 AN: 5168

South Asian (SAS) AF: 0.294 AC: 1410 AN: 4804

European-Finnish (FIN) AF: 0.0413 AC: 438 AN: 10618

Middle Eastern (MID) AF: 0.126 AC: 37 AN: 294

European-Non Finnish (NFE) AF: 0.0880 AC: 5980 AN: 67992

Other (OTH) AF: 0.150 AC: 316 AN: 2106

Alfa AF: 0.115 Hom.: 4718

Bravo AF: 0.167

Asia WGS AF: 0.299 AC: 1041 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.33
DANN	Benign	0.43
PhyloP100		-2.0

Splicing

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

Other links and lift over

dbSNP: rs7581710; hg19: chr2-121195181;