2-36671467-C-G

Variant names:

• chr2-36671467-C-G
• rs10490668

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 0.376 in 140,902 control chromosomes in the GnomAD database, including 10,220 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 0.38 (10220 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0480
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.541 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: 0.377 AC: 53010 AN: 140784 Hom.: 10222 Cov.: 31

Gnomad AFR AF: 0.191

Gnomad AMI AF: 0.393

Gnomad AMR AF: 0.389

Gnomad ASJ AF: 0.581

Gnomad EAS AF: 0.409

Gnomad SAS AF: 0.559

Gnomad FIN AF: 0.444

Gnomad MID AF: 0.539

Gnomad NFE AF: 0.448

Gnomad OTH AF: 0.409

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

GnomAD4 genome AF: 0.376 AC: 53004 AN: 140902 Hom.: 10220 Cov.: 31 AF XY: 0.380 AC XY: 25896 AN XY: 68232

African (AFR) AF: 0.191 AC: 7406 AN: 38784

American (AMR) AF: 0.389 AC: 5160 AN: 13278

Ashkenazi Jewish (ASJ) AF: 0.581 AC: 1970 AN: 3390

East Asian (EAS) AF: 0.409 AC: 1878 AN: 4596

South Asian (SAS) AF: 0.559 AC: 2455 AN: 4392

European-Finnish (FIN) AF: 0.444 AC: 4160 AN: 9362

Middle Eastern (MID) AF: 0.532 AC: 151 AN: 284

European-Non Finnish (NFE) AF: 0.448 AC: 28696 AN: 64006

Other (OTH) AF: 0.405 AC: 784 AN: 1934

Alfa AF: 0.242 Hom.: 615

Bravo AF: 0.333

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.5
DANN	Benign	0.25
PhyloP100		0.048

Splicing

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

Other links and lift over

dbSNP: rs10490668; hg19: chr2-36898610;