2-160097449-T-C

Variant names:

• chr2-160097449-T-C
• rs4129787

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 0.788 in 151,908 control chromosomes in the GnomAD database, including 48,115 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 0.79 (48115 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.73
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.936 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: 0.788 AC: 119599 AN: 151790 Hom.: 48059 Cov.: 29

Gnomad AFR AF: 0.943

Gnomad AMI AF: 0.559

Gnomad AMR AF: 0.814

Gnomad ASJ AF: 0.606

Gnomad EAS AF: 0.774

Gnomad SAS AF: 0.641

Gnomad FIN AF: 0.739

Gnomad MID AF: 0.623

Gnomad NFE AF: 0.721

Gnomad OTH AF: 0.739

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

GnomAD4 genome AF: 0.788 AC: 119719 AN: 151908 Hom.: 48115 Cov.: 29 AF XY: 0.789 AC XY: 58538 AN XY: 74208

African (AFR) AF: 0.943 AC: 39114 AN: 41462

American (AMR) AF: 0.814 AC: 12427 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.606 AC: 2103 AN: 3468

East Asian (EAS) AF: 0.773 AC: 3969 AN: 5132

South Asian (SAS) AF: 0.641 AC: 3072 AN: 4796

European-Finnish (FIN) AF: 0.739 AC: 7786 AN: 10534

Middle Eastern (MID) AF: 0.629 AC: 185 AN: 294

European-Non Finnish (NFE) AF: 0.721 AC: 48994 AN: 67940

Other (OTH) AF: 0.740 AC: 1559 AN: 2106

Alfa AF: 0.767 Hom.: 5866

Bravo AF: 0.804

Asia WGS AF: 0.742 AC: 2582 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.49
DANN	Benign	0.83
PhyloP100		-2.7

Splicing

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

Other links and lift over

dbSNP: rs4129787; hg19: chr2-160953960;