rs4075810

Variant names:

• chr2-136245575-C-T
• rs4075810

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 0.142 in 152,082 control chromosomes in the GnomAD database, including 1,987 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 0.14 (1987 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.54
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.394 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: 0.142 AC: 21566 AN: 151964 Hom.: 1985 Cov.: 31

Gnomad AFR AF: 0.0989

Gnomad AMI AF: 0.0791

Gnomad AMR AF: 0.218

Gnomad ASJ AF: 0.211

Gnomad EAS AF: 0.410

Gnomad SAS AF: 0.263

Gnomad FIN AF: 0.130

Gnomad MID AF: 0.282

Gnomad NFE AF: 0.120

Gnomad OTH AF: 0.178

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

GnomAD4 genome AF: 0.142 AC: 21596 AN: 152082 Hom.: 1987 Cov.: 31 AF XY: 0.149 AC XY: 11064 AN XY: 74350

African (AFR) AF: 0.0991 AC: 4113 AN: 41486

American (AMR) AF: 0.219 AC: 3337 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.211 AC: 732 AN: 3470

East Asian (EAS) AF: 0.409 AC: 2109 AN: 5160

South Asian (SAS) AF: 0.263 AC: 1267 AN: 4818

European-Finnish (FIN) AF: 0.130 AC: 1371 AN: 10572

Middle Eastern (MID) AF: 0.279 AC: 82 AN: 294

European-Non Finnish (NFE) AF: 0.120 AC: 8127 AN: 67990

Other (OTH) AF: 0.183 AC: 386 AN: 2112

Alfa AF: 0.135 Hom.: 2706

Bravo AF: 0.146

Asia WGS AF: 0.359 AC: 1246 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.58
DANN	Benign	0.57
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs4075810; hg19: chr2-137003145;