rs7579944

Variant names:

• chr2-30222160-T-C
• rs7579944

Your query was ambiguous. Multiple possible variants found:

• chr2-30222160-T-C
• chr2-30222160-T-G

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 0.517 in 152,050 control chromosomes in the GnomAD database, including 22,097 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 0.52 (22097 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.403

ACMG classification

Verdict is Benign. Variant got -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 = 0.623 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: 0.517 AC: 78543 AN: 151932 Hom.: 22094 Cov.: 32

Gnomad AFR AF: 0.285

Gnomad AMI AF: 0.593

Gnomad AMR AF: 0.620

Gnomad ASJ AF: 0.673

Gnomad EAS AF: 0.357

Gnomad SAS AF: 0.510

Gnomad FIN AF: 0.575

Gnomad MID AF: 0.661

Gnomad NFE AF: 0.628

Gnomad OTH AF: 0.545

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

GnomAD4 genome AF: 0.517 AC: 78571 AN: 152050 Hom.: 22097 Cov.: 32 AF XY: 0.516 AC XY: 38352 AN XY: 74340

Gnomad4 AFR AF: 0.285

Gnomad4 AMR AF: 0.619

Gnomad4 ASJ AF: 0.673

Gnomad4 EAS AF: 0.357

Gnomad4 SAS AF: 0.511

Gnomad4 FIN AF: 0.575

Gnomad4 NFE AF: 0.628

Gnomad4 OTH AF: 0.546

Alfa AF: 0.610 Hom.: 64817

Bravo AF: 0.513

Asia WGS AF: 0.428 AC: 1489 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	3.7
DANN	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7579944; hg19: chr2-30445026;