2-60232671-T-C

Variant names:

• chr2-60232671-T-C
• rs359268

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 0.477 in 151,714 control chromosomes in the GnomAD database, including 17,407 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 0.48 (17407 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.346
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.501 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: 0.477 AC: 72264 AN: 151596 Hom.: 17400 Cov.: 32

Gnomad AFR AF: 0.441

Gnomad AMI AF: 0.534

Gnomad AMR AF: 0.500

Gnomad ASJ AF: 0.486

Gnomad EAS AF: 0.381

Gnomad SAS AF: 0.364

Gnomad FIN AF: 0.484

Gnomad MID AF: 0.497

Gnomad NFE AF: 0.505

Gnomad OTH AF: 0.501

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

GnomAD4 genome AF: 0.477 AC: 72310 AN: 151714 Hom.: 17407 Cov.: 32 AF XY: 0.472 AC XY: 34968 AN XY: 74154

African (AFR) AF: 0.441 AC: 18221 AN: 41314

American (AMR) AF: 0.500 AC: 7634 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.486 AC: 1686 AN: 3466

East Asian (EAS) AF: 0.382 AC: 1973 AN: 5168

South Asian (SAS) AF: 0.364 AC: 1751 AN: 4808

European-Finnish (FIN) AF: 0.484 AC: 5068 AN: 10480

Middle Eastern (MID) AF: 0.500 AC: 147 AN: 294

European-Non Finnish (NFE) AF: 0.505 AC: 34295 AN: 67912

Other (OTH) AF: 0.498 AC: 1049 AN: 2108

Alfa AF: 0.455 Hom.: 5761

Bravo AF: 0.484

Asia WGS AF: 0.355 AC: 1226 AN: 3450

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	3.1
DANN	Benign	0.87
PhyloP100		-0.35

Splicing

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

Other links and lift over

dbSNP: rs359268; hg19: chr2-60459806; COSMIC: COSV107164886;