chr2-201179993-G-A

Variant names:

• chr2-201179993-G-A
• rs11900753

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 0.118 in 152,070 control chromosomes in the GnomAD database, including 2,239 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 0.12 (2239 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.938
• Publications: 11 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.314 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: 0.118 AC: 17897 AN: 151952 Hom.: 2219 Cov.: 32

Gnomad AFR AF: 0.318

Gnomad AMI AF: 0.00768

Gnomad AMR AF: 0.0544

Gnomad ASJ AF: 0.0911

Gnomad EAS AF: 0.00423

Gnomad SAS AF: 0.0613

Gnomad FIN AF: 0.0329

Gnomad MID AF: 0.0949

Gnomad NFE AF: 0.0401

Gnomad OTH AF: 0.0842

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

GnomAD4 genome AF: 0.118 AC: 17971 AN: 152070 Hom.: 2239 Cov.: 32 AF XY: 0.115 AC XY: 8583 AN XY: 74340

African (AFR) AF: 0.319 AC: 13206 AN: 41414

American (AMR) AF: 0.0543 AC: 830 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.0911 AC: 316 AN: 3470

East Asian (EAS) AF: 0.00424 AC: 22 AN: 5184

South Asian (SAS) AF: 0.0608 AC: 293 AN: 4822

European-Finnish (FIN) AF: 0.0329 AC: 348 AN: 10590

Middle Eastern (MID) AF: 0.102 AC: 30 AN: 294

European-Non Finnish (NFE) AF: 0.0401 AC: 2725 AN: 67988

Other (OTH) AF: 0.0919 AC: 194 AN: 2112

Alfa AF: 0.0628 Hom.: 2317

Bravo AF: 0.125

Asia WGS AF: 0.0720 AC: 250 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.75
DANN	Benign	0.22
PhyloP100		-0.94

Splicing

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

Other links and lift over

dbSNP: rs11900753; hg19: chr2-202044716;