chr2-60740935-G-T

Variant names:

• chr2-60740935-G-T
• rs7579240

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 0.247 in 151,198 control chromosomes in the GnomAD database, including 5,072 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 0.25 (5072 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.928
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.295 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: 0.247 AC: 37384 AN: 151100 Hom.: 5070 Cov.: 30

Gnomad AFR AF: 0.170

Gnomad AMI AF: 0.176

Gnomad AMR AF: 0.234

Gnomad ASJ AF: 0.264

Gnomad EAS AF: 0.108

Gnomad SAS AF: 0.122

Gnomad FIN AF: 0.366

Gnomad MID AF: 0.340

Gnomad NFE AF: 0.298

Gnomad OTH AF: 0.259

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

GnomAD4 genome AF: 0.247 AC: 37393 AN: 151198 Hom.: 5072 Cov.: 30 AF XY: 0.248 AC XY: 18326 AN XY: 73794

African (AFR) AF: 0.170 AC: 6987 AN: 41190

American (AMR) AF: 0.234 AC: 3537 AN: 15146

Ashkenazi Jewish (ASJ) AF: 0.264 AC: 915 AN: 3462

East Asian (EAS) AF: 0.109 AC: 560 AN: 5150

South Asian (SAS) AF: 0.121 AC: 580 AN: 4786

European-Finnish (FIN) AF: 0.366 AC: 3785 AN: 10344

Middle Eastern (MID) AF: 0.355 AC: 103 AN: 290

European-Non Finnish (NFE) AF: 0.298 AC: 20232 AN: 67830

Other (OTH) AF: 0.255 AC: 534 AN: 2092

Alfa AF: 0.278 Hom.: 26042

Bravo AF: 0.236

Asia WGS AF: 0.112 AC: 388 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.24
DANN	Benign	0.45
PhyloP100		-0.93

Splicing

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

Other links and lift over

dbSNP: rs7579240; hg19: chr2-60968070;