2-155723148-T-G

Variant names:

• chr2-155723148-T-G
• rs4664774

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 0.802 in 151,724 control chromosomes in the GnomAD database, including 49,181 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 0.80 (49181 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.19
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.949 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: 0.802 AC: 121614 AN: 151606 Hom.: 49139 Cov.: 31

Gnomad AFR AF: 0.708

Gnomad AMI AF: 0.750

Gnomad AMR AF: 0.864

Gnomad ASJ AF: 0.769

Gnomad EAS AF: 0.971

Gnomad SAS AF: 0.960

Gnomad FIN AF: 0.821

Gnomad MID AF: 0.845

Gnomad NFE AF: 0.820

Gnomad OTH AF: 0.825

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

GnomAD4 genome AF: 0.802 AC: 121710 AN: 151724 Hom.: 49181 Cov.: 31 AF XY: 0.810 AC XY: 60012 AN XY: 74130

African (AFR) AF: 0.709 AC: 29315 AN: 41376

American (AMR) AF: 0.864 AC: 13160 AN: 15236

Ashkenazi Jewish (ASJ) AF: 0.769 AC: 2667 AN: 3466

East Asian (EAS) AF: 0.971 AC: 5014 AN: 5164

South Asian (SAS) AF: 0.960 AC: 4624 AN: 4816

European-Finnish (FIN) AF: 0.821 AC: 8626 AN: 10506

Middle Eastern (MID) AF: 0.847 AC: 249 AN: 294

European-Non Finnish (NFE) AF: 0.820 AC: 55639 AN: 67858

Other (OTH) AF: 0.826 AC: 1735 AN: 2100

Alfa AF: 0.819 Hom.: 14801

Bravo AF: 0.799

Asia WGS AF: 0.937 AC: 3224 AN: 3440

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.091
DANN	Benign	0.48
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs4664774; hg19: chr2-156579660;