rs7567619

Variant names:

• chr2-112807389-T-A
• rs7567619

Your query was ambiguous. Multiple possible variants found:

• chr2-112807389-T-A
• chr2-112807389-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 0.311 in 150,684 control chromosomes in the GnomAD database, including 7,930 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 0.31 (7930 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.26

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 (EAS) allele frequency at 95% confidence interval = 0.683 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: 0.311 AC: 46754 AN: 150576 Hom.: 7914 Cov.: 29

Gnomad AFR AF: 0.230

Gnomad AMI AF: 0.264

Gnomad AMR AF: 0.393

Gnomad ASJ AF: 0.254

Gnomad EAS AF: 0.701

Gnomad SAS AF: 0.333

Gnomad FIN AF: 0.396

Gnomad MID AF: 0.213

Gnomad NFE AF: 0.301

Gnomad OTH AF: 0.316

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

GnomAD4 genome AF: 0.311 AC: 46792 AN: 150684 Hom.: 7930 Cov.: 29 AF XY: 0.319 AC XY: 23465 AN XY: 73532

Gnomad4 AFR AF: 0.230

Gnomad4 AMR AF: 0.394

Gnomad4 ASJ AF: 0.254

Gnomad4 EAS AF: 0.702

Gnomad4 SAS AF: 0.333

Gnomad4 FIN AF: 0.396

Gnomad4 NFE AF: 0.301

Gnomad4 OTH AF: 0.320

Alfa AF: 0.137 Hom.: 265

Bravo AF: 0.313

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	5.3
DANN	Benign	0.32

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7567619; hg19: chr2-113564966;