1-91946003-T-C

Variant names:

• chr1-91946003-T-C
• rs6656817

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 0.84 in 148,608 control chromosomes in the GnomAD database, including 53,650 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 0.84 (53650 hom., cov: 23)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.19
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.929 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: 0.840 AC: 124721 AN: 148510 Hom.: 53637 Cov.: 23

Gnomad AFR AF: 0.657

Gnomad AMI AF: 0.971

Gnomad AMR AF: 0.873

Gnomad ASJ AF: 0.937

Gnomad EAS AF: 0.602

Gnomad SAS AF: 0.836

Gnomad FIN AF: 0.957

Gnomad MID AF: 0.901

Gnomad NFE AF: 0.935

Gnomad OTH AF: 0.840

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

GnomAD4 genome AF: 0.840 AC: 124767 AN: 148608 Hom.: 53650 Cov.: 23 AF XY: 0.841 AC XY: 60804 AN XY: 72274

African (AFR) AF: 0.657 AC: 26389 AN: 40192

American (AMR) AF: 0.873 AC: 13009 AN: 14902

Ashkenazi Jewish (ASJ) AF: 0.937 AC: 3226 AN: 3442

East Asian (EAS) AF: 0.601 AC: 3008 AN: 5004

South Asian (SAS) AF: 0.836 AC: 3862 AN: 4620

European-Finnish (FIN) AF: 0.957 AC: 9504 AN: 9936

Middle Eastern (MID) AF: 0.901 AC: 265 AN: 294

European-Non Finnish (NFE) AF: 0.935 AC: 62904 AN: 67248

Other (OTH) AF: 0.833 AC: 1722 AN: 2066

Alfa AF: 0.885 Hom.: 7013

Bravo AF: 0.825

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.6
DANN	Benign	0.49
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs6656817; hg19: chr1-92411560;