rs7567386

Variant names:

• chr2-41219469-T-G
• rs7567386

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 0.701 in 151,990 control chromosomes in the GnomAD database, including 37,663 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 0.70 (37663 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.24

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.75 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: 0.701 AC: 106536 AN: 151870 Hom.: 37644 Cov.: 32

Gnomad AFR AF: 0.757

Gnomad AMI AF: 0.577

Gnomad AMR AF: 0.644

Gnomad ASJ AF: 0.777

Gnomad EAS AF: 0.531

Gnomad SAS AF: 0.768

Gnomad FIN AF: 0.725

Gnomad MID AF: 0.820

Gnomad NFE AF: 0.683

Gnomad OTH AF: 0.699

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

GnomAD4 genome AF: 0.701 AC: 106608 AN: 151990 Hom.: 37663 Cov.: 32 AF XY: 0.702 AC XY: 52124 AN XY: 74298

Gnomad4 AFR AF: 0.757

Gnomad4 AMR AF: 0.644

Gnomad4 ASJ AF: 0.777

Gnomad4 EAS AF: 0.531

Gnomad4 SAS AF: 0.767

Gnomad4 FIN AF: 0.725

Gnomad4 NFE AF: 0.683

Gnomad4 OTH AF: 0.696

Alfa AF: 0.687 Hom.: 74387

Bravo AF: 0.693

Asia WGS AF: 0.643 AC: 2236 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.65
DANN	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7567386; hg19: chr2-41446609;