rs7581178

Variant names:

• chr2-120352811-G-C
• rs7581178

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 0.0933 in 152,292 control chromosomes in the GnomAD database, including 924 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 0.093 (924 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.452
• 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 (SAS) allele frequency at 95% confidence interval = 0.203 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: 0.0933 AC: 14197 AN: 152174 Hom.: 920 Cov.: 33

Gnomad AFR AF: 0.159

Gnomad AMI AF: 0.0274

Gnomad AMR AF: 0.0546

Gnomad ASJ AF: 0.108

Gnomad EAS AF: 0.156

Gnomad SAS AF: 0.214

Gnomad FIN AF: 0.0436

Gnomad MID AF: 0.104

Gnomad NFE AF: 0.0571

Gnomad OTH AF: 0.0750

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

GnomAD4 genome AF: 0.0933 AC: 14211 AN: 152292 Hom.: 924 Cov.: 33 AF XY: 0.0951 AC XY: 7079 AN XY: 74474

African (AFR) AF: 0.159 AC: 6592 AN: 41544

American (AMR) AF: 0.0545 AC: 834 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.108 AC: 376 AN: 3472

East Asian (EAS) AF: 0.156 AC: 808 AN: 5178

South Asian (SAS) AF: 0.214 AC: 1030 AN: 4822

European-Finnish (FIN) AF: 0.0436 AC: 463 AN: 10626

Middle Eastern (MID) AF: 0.109 AC: 32 AN: 294

European-Non Finnish (NFE) AF: 0.0571 AC: 3884 AN: 68026

Other (OTH) AF: 0.0789 AC: 167 AN: 2116

Alfa AF: 0.0688 Hom.: 71

Bravo AF: 0.0924

Asia WGS AF: 0.233 AC: 809 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	1.7
DANN	Benign	0.66
PhyloP100		0.45

Splicing

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

Other links and lift over

dbSNP: rs7581178; hg19: chr2-121110387;