2-149540704-G-T

Variant names:

• chr2-149540704-G-T
• rs7578361

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 0.661 in 152,094 control chromosomes in the GnomAD database, including 36,286 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 0.66 (36286 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.102
• 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 (EAS) allele frequency at 95% confidence interval = 0.834 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: 0.661 AC: 100531 AN: 151976 Hom.: 36278 Cov.: 33

Gnomad AFR AF: 0.349

Gnomad AMI AF: 0.755

Gnomad AMR AF: 0.667

Gnomad ASJ AF: 0.813

Gnomad EAS AF: 0.855

Gnomad SAS AF: 0.764

Gnomad FIN AF: 0.849

Gnomad MID AF: 0.729

Gnomad NFE AF: 0.789

Gnomad OTH AF: 0.684

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

GnomAD4 genome AF: 0.661 AC: 100559 AN: 152094 Hom.: 36286 Cov.: 33 AF XY: 0.665 AC XY: 49472 AN XY: 74344

African (AFR) AF: 0.348 AC: 14444 AN: 41484

American (AMR) AF: 0.667 AC: 10180 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.813 AC: 2820 AN: 3470

East Asian (EAS) AF: 0.855 AC: 4417 AN: 5164

South Asian (SAS) AF: 0.765 AC: 3689 AN: 4822

European-Finnish (FIN) AF: 0.849 AC: 9005 AN: 10604

Middle Eastern (MID) AF: 0.729 AC: 213 AN: 292

European-Non Finnish (NFE) AF: 0.789 AC: 53657 AN: 67972

Other (OTH) AF: 0.684 AC: 1447 AN: 2114

Alfa AF: 0.736 Hom.: 83939

Bravo AF: 0.633

Asia WGS AF: 0.794 AC: 2758 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	1.9
DANN	Benign	0.80
PhyloP100		-0.10

Splicing

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

Other links and lift over

dbSNP: rs7578361; hg19: chr2-150397218;