rs7581219

Positions:

• chr2-173498846-G-A
• chr2-173498846-G-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.387 in 151,986 control chromosomes in the GnomAD database, including 11,516 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 0.39 (11516 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.539

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.424 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.387 AC: 58814 AN: 151868 Hom.: 11517 Cov.: 32

Gnomad AFR AF: 0.429

Gnomad AMI AF: 0.502

Gnomad AMR AF: 0.362

Gnomad ASJ AF: 0.460

Gnomad EAS AF: 0.320

Gnomad SAS AF: 0.389

Gnomad FIN AF: 0.282

Gnomad MID AF: 0.500

Gnomad NFE AF: 0.382

Gnomad OTH AF: 0.427

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

GnomAD4 genome AF: 0.387 AC: 58832 AN: 151986 Hom.: 11516 Cov.: 32 AF XY: 0.382 AC XY: 28393 AN XY: 74280

Gnomad4 AFR AF: 0.430

Gnomad4 AMR AF: 0.362

Gnomad4 ASJ AF: 0.460

Gnomad4 EAS AF: 0.319

Gnomad4 SAS AF: 0.387

Gnomad4 FIN AF: 0.282

Gnomad4 NFE AF: 0.382

Gnomad4 OTH AF: 0.421

Alfa AF: 0.377 Hom.: 4723

Bravo AF: 0.396

Asia WGS AF: 0.333 AC: 1161 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.3
DANN	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7581219; hg19: chr2-174363574;