2-36078096-T-C

Variant names:

• chr2-36078096-T-C
• rs4670136

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 0.111 in 152,024 control chromosomes in the GnomAD database, including 1,793 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 0.11 (1793 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.293
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.251 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: 0.110 AC: 16764 AN: 151908 Hom.: 1766 Cov.: 32

Gnomad AFR AF: 0.254

Gnomad AMI AF: 0.00440

Gnomad AMR AF: 0.208

Gnomad ASJ AF: 0.0156

Gnomad EAS AF: 0.104

Gnomad SAS AF: 0.0239

Gnomad FIN AF: 0.0243

Gnomad MID AF: 0.0127

Gnomad NFE AF: 0.0286

Gnomad OTH AF: 0.0941

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

GnomAD4 genome AF: 0.111 AC: 16841 AN: 152024 Hom.: 1793 Cov.: 32 AF XY: 0.111 AC XY: 8220 AN XY: 74302

African (AFR) AF: 0.255 AC: 10549 AN: 41436

American (AMR) AF: 0.209 AC: 3182 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.0156 AC: 54 AN: 3472

East Asian (EAS) AF: 0.104 AC: 535 AN: 5156

South Asian (SAS) AF: 0.0235 AC: 113 AN: 4816

European-Finnish (FIN) AF: 0.0243 AC: 258 AN: 10600

Middle Eastern (MID) AF: 0.0102 AC: 3 AN: 294

European-Non Finnish (NFE) AF: 0.0286 AC: 1947 AN: 67990

Other (OTH) AF: 0.0932 AC: 196 AN: 2104

Alfa AF: 0.0451 Hom.: 489

Bravo AF: 0.134

Asia WGS AF: 0.0980 AC: 343 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.7
DANN	Benign	0.40
PhyloP100		-0.29

Splicing

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

Other links and lift over

dbSNP: rs4670136; hg19: chr2-36305239;