2-85313960-T-C

Variant names:

• chr2-85313960-T-C
• rs4832163

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 0.559 in 151,986 control chromosomes in the GnomAD database, including 24,280 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 0.56 (24280 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.308
• Publications: 14 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 (EAS) allele frequency at 95% confidence interval = 0.853 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: 0.559 AC: 84904 AN: 151868 Hom.: 24267 Cov.: 32

Gnomad AFR AF: 0.526

Gnomad AMI AF: 0.529

Gnomad AMR AF: 0.662

Gnomad ASJ AF: 0.640

Gnomad EAS AF: 0.875

Gnomad SAS AF: 0.640

Gnomad FIN AF: 0.585

Gnomad MID AF: 0.677

Gnomad NFE AF: 0.517

Gnomad OTH AF: 0.586

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

GnomAD4 genome AF: 0.559 AC: 84951 AN: 151986 Hom.: 24280 Cov.: 32 AF XY: 0.567 AC XY: 42137 AN XY: 74304

African (AFR) AF: 0.525 AC: 21754 AN: 41426

American (AMR) AF: 0.662 AC: 10108 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.640 AC: 2222 AN: 3470

East Asian (EAS) AF: 0.874 AC: 4512 AN: 5160

South Asian (SAS) AF: 0.639 AC: 3079 AN: 4820

European-Finnish (FIN) AF: 0.585 AC: 6190 AN: 10576

Middle Eastern (MID) AF: 0.694 AC: 204 AN: 294

European-Non Finnish (NFE) AF: 0.517 AC: 35161 AN: 67952

Other (OTH) AF: 0.587 AC: 1239 AN: 2110

Alfa AF: 0.534 Hom.: 20522

Bravo AF: 0.568

Asia WGS AF: 0.756 AC: 2626 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	2.6
DANN	Benign	0.60
PhyloP100		0.31

Splicing

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

Other links and lift over

dbSNP: rs4832163; hg19: chr2-85541083;