rs1192415

Variant names:

• chr1-91611540-G-A
• rs1192415

Your query was ambiguous. Multiple possible variants found:

• chr1-91611540-G-A
• chr1-91611540-G-C
• chr1-91611540-G-T

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 0.807 in 151,948 control chromosomes in the GnomAD database, including 49,616 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 0.81 (49616 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.317
• Publications: 49 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.842 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: 0.807 AC: 122501 AN: 151830 Hom.: 49580 Cov.: 30

Gnomad AFR AF: 0.815

Gnomad AMI AF: 0.791

Gnomad AMR AF: 0.739

Gnomad ASJ AF: 0.800

Gnomad EAS AF: 0.864

Gnomad SAS AF: 0.716

Gnomad FIN AF: 0.833

Gnomad MID AF: 0.759

Gnomad NFE AF: 0.816

Gnomad OTH AF: 0.805

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

GnomAD4 genome AF: 0.807 AC: 122590 AN: 151948 Hom.: 49616 Cov.: 30 AF XY: 0.807 AC XY: 59928 AN XY: 74254

African (AFR) AF: 0.816 AC: 33788 AN: 41416

American (AMR) AF: 0.739 AC: 11284 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.800 AC: 2778 AN: 3472

East Asian (EAS) AF: 0.863 AC: 4436 AN: 5140

South Asian (SAS) AF: 0.714 AC: 3445 AN: 4826

European-Finnish (FIN) AF: 0.833 AC: 8763 AN: 10518

Middle Eastern (MID) AF: 0.765 AC: 225 AN: 294

European-Non Finnish (NFE) AF: 0.816 AC: 55452 AN: 67986

Other (OTH) AF: 0.804 AC: 1699 AN: 2112

Alfa AF: 0.813 Hom.: 162898

Bravo AF: 0.803

Asia WGS AF: 0.786 AC: 2732 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	10
DANN	Benign	0.77
PhyloP100		0.32

Splicing

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

Other links and lift over

dbSNP: rs1192415; hg19: chr1-92077097;