chr2-226236695-A-G

Variant names:

• chr2-226236695-A-G
• rs2972144

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 0.691 in 152,054 control chromosomes in the GnomAD database, including 36,566 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 0.69 (36566 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.506
• Publications: 29 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.905 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: 0.691 AC: 104914 AN: 151936 Hom.: 36522 Cov.: 32

Gnomad AFR AF: 0.735

Gnomad AMI AF: 0.567

Gnomad AMR AF: 0.744

Gnomad ASJ AF: 0.712

Gnomad EAS AF: 0.927

Gnomad SAS AF: 0.770

Gnomad FIN AF: 0.628

Gnomad MID AF: 0.538

Gnomad NFE AF: 0.639

Gnomad OTH AF: 0.675

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

GnomAD4 genome AF: 0.691 AC: 105013 AN: 152054 Hom.: 36566 Cov.: 32 AF XY: 0.692 AC XY: 51391 AN XY: 74314

African (AFR) AF: 0.735 AC: 30484 AN: 41474

American (AMR) AF: 0.744 AC: 11369 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.712 AC: 2468 AN: 3468

East Asian (EAS) AF: 0.927 AC: 4799 AN: 5176

South Asian (SAS) AF: 0.770 AC: 3712 AN: 4818

European-Finnish (FIN) AF: 0.628 AC: 6614 AN: 10538

Middle Eastern (MID) AF: 0.537 AC: 158 AN: 294

European-Non Finnish (NFE) AF: 0.639 AC: 43459 AN: 67990

Other (OTH) AF: 0.679 AC: 1435 AN: 2114

Alfa AF: 0.667 Hom.: 13992

Bravo AF: 0.702

Asia WGS AF: 0.851 AC: 2957 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	7.5
DANN	Benign	0.84
PhyloP100		0.51

Splicing

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

Other links and lift over

dbSNP: rs2972144; hg19: chr2-227101411;