chr2-237858561-A-T

Variant names:

• chr2-237858561-A-T
• rs3754701

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 0.431 in 152,042 control chromosomes in the GnomAD database, including 14,679 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 0.43 (14679 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.79
• Publications: 15 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.539 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: 0.431 AC: 65501 AN: 151924 Hom.: 14645 Cov.: 33

Gnomad AFR AF: 0.528

Gnomad AMI AF: 0.440

Gnomad AMR AF: 0.493

Gnomad ASJ AF: 0.334

Gnomad EAS AF: 0.556

Gnomad SAS AF: 0.515

Gnomad FIN AF: 0.378

Gnomad MID AF: 0.408

Gnomad NFE AF: 0.357

Gnomad OTH AF: 0.409

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

GnomAD4 genome AF: 0.431 AC: 65596 AN: 152042 Hom.: 14679 Cov.: 33 AF XY: 0.435 AC XY: 32317 AN XY: 74310

African (AFR) AF: 0.529 AC: 21923 AN: 41462

American (AMR) AF: 0.493 AC: 7537 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.334 AC: 1159 AN: 3472

East Asian (EAS) AF: 0.556 AC: 2867 AN: 5152

South Asian (SAS) AF: 0.514 AC: 2479 AN: 4826

European-Finnish (FIN) AF: 0.378 AC: 3991 AN: 10554

Middle Eastern (MID) AF: 0.415 AC: 122 AN: 294

European-Non Finnish (NFE) AF: 0.357 AC: 24238 AN: 67970

Other (OTH) AF: 0.416 AC: 879 AN: 2114

Alfa AF: 0.234 Hom.: 502

Bravo AF: 0.444

Asia WGS AF: 0.601 AC: 2091 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.32
DANN	Benign	0.69
PhyloP100		-2.8
PromoterAI		0.056	Neutral

Splicing

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

Other links and lift over

dbSNP: rs3754701; hg19: chr2-238767204;