2-60635739-C-T

Variant names:

• chr2-60635739-C-T
• rs1467068

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 0.353 in 151,726 control chromosomes in the GnomAD database, including 10,356 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 0.35 (10356 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.167
• Publications: 4 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 = 0.507 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: 0.353 AC: 53558 AN: 151608 Hom.: 10328 Cov.: 31

Gnomad AFR AF: 0.512

Gnomad AMI AF: 0.297

Gnomad AMR AF: 0.327

Gnomad ASJ AF: 0.282

Gnomad EAS AF: 0.110

Gnomad SAS AF: 0.183

Gnomad FIN AF: 0.296

Gnomad MID AF: 0.228

Gnomad NFE AF: 0.308

Gnomad OTH AF: 0.328

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

GnomAD4 genome AF: 0.353 AC: 53632 AN: 151726 Hom.: 10356 Cov.: 31 AF XY: 0.347 AC XY: 25712 AN XY: 74138

African (AFR) AF: 0.512 AC: 21189 AN: 41354

American (AMR) AF: 0.328 AC: 4993 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.282 AC: 977 AN: 3470

East Asian (EAS) AF: 0.110 AC: 569 AN: 5164

South Asian (SAS) AF: 0.184 AC: 882 AN: 4798

European-Finnish (FIN) AF: 0.296 AC: 3113 AN: 10504

Middle Eastern (MID) AF: 0.224 AC: 66 AN: 294

European-Non Finnish (NFE) AF: 0.308 AC: 20890 AN: 67886

Other (OTH) AF: 0.324 AC: 683 AN: 2106

Alfa AF: 0.316 Hom.: 9932

Bravo AF: 0.364

Asia WGS AF: 0.159 AC: 555 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	4.6
DANN	Benign	0.64
PhyloP100		0.17

Splicing

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

Other links and lift over

dbSNP: rs1467068; hg19: chr2-60862874;