2-210706903-T-C

Variant names:

• chr2-210706903-T-C
• rs4673548

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 0.56 in 152,012 control chromosomes in the GnomAD database, including 25,237 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 (25237 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.300
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.836 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.560 AC: 85132 AN: 151894 Hom.: 25233 Cov.: 31

Gnomad AFR AF: 0.362

Gnomad AMI AF: 0.514

Gnomad AMR AF: 0.653

Gnomad ASJ AF: 0.678

Gnomad EAS AF: 0.857

Gnomad SAS AF: 0.603

Gnomad FIN AF: 0.662

Gnomad MID AF: 0.636

Gnomad NFE AF: 0.613

Gnomad OTH AF: 0.574

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

GnomAD4 genome AF: 0.560 AC: 85161 AN: 152012 Hom.: 25237 Cov.: 31 AF XY: 0.565 AC XY: 42005 AN XY: 74318

African (AFR) AF: 0.362 AC: 15014 AN: 41454

American (AMR) AF: 0.654 AC: 9989 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.678 AC: 2351 AN: 3468

East Asian (EAS) AF: 0.857 AC: 4403 AN: 5138

South Asian (SAS) AF: 0.604 AC: 2908 AN: 4818

European-Finnish (FIN) AF: 0.662 AC: 6988 AN: 10562

Middle Eastern (MID) AF: 0.633 AC: 186 AN: 294

European-Non Finnish (NFE) AF: 0.613 AC: 41647 AN: 67978

Other (OTH) AF: 0.572 AC: 1208 AN: 2112

Alfa AF: 0.477 Hom.: 1509

Bravo AF: 0.554

Asia WGS AF: 0.670 AC: 2328 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	5.0
DANN	Benign	0.62
PhyloP100		0.30

Splicing

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

Other links and lift over

dbSNP: rs4673548; hg19: chr2-211571627;