chr2-102418289-A-G

Variant names:

• chr2-102418289-A-G
• rs4851581

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 0.0625 in 152,264 control chromosomes in the GnomAD database, including 446 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 0.062 (446 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.309
• Publications: 9 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0865 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: 0.0626 AC: 9520 AN: 152146 Hom.: 446 Cov.: 33

Gnomad AFR AF: 0.0150

Gnomad AMI AF: 0.0868

Gnomad AMR AF: 0.0545

Gnomad ASJ AF: 0.0470

Gnomad EAS AF: 0.000193

Gnomad SAS AF: 0.0153

Gnomad FIN AF: 0.151

Gnomad MID AF: 0.0285

Gnomad NFE AF: 0.0884

Gnomad OTH AF: 0.0645

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

GnomAD4 genome AF: 0.0625 AC: 9516 AN: 152264 Hom.: 446 Cov.: 33 AF XY: 0.0638 AC XY: 4747 AN XY: 74442

African (AFR) AF: 0.0149 AC: 620 AN: 41580

American (AMR) AF: 0.0544 AC: 833 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.0470 AC: 163 AN: 3466

East Asian (EAS) AF: 0.000193 AC: 1 AN: 5174

South Asian (SAS) AF: 0.0153 AC: 74 AN: 4830

European-Finnish (FIN) AF: 0.151 AC: 1592 AN: 10574

Middle Eastern (MID) AF: 0.0306 AC: 9 AN: 294

European-Non Finnish (NFE) AF: 0.0884 AC: 6010 AN: 68016

Other (OTH) AF: 0.0638 AC: 135 AN: 2116

Alfa AF: 0.0733 Hom.: 79

Bravo AF: 0.0536

Asia WGS AF: 0.00837 AC: 30 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	0.42
DANN	Benign	0.60
PhyloP100		-0.31
PromoterAI		-0.0087	Neutral

Splicing

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

Other links and lift over

dbSNP: rs4851581; hg19: chr2-103034749;