1-91656775-A-C

Variant names:

• chr1-91656775-A-C
• rs2148322

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 0.736 in 152,142 control chromosomes in the GnomAD database, including 41,967 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 0.74 (41967 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.344
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.897 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: 0.736 AC: 111857 AN: 152022 Hom.: 41951 Cov.: 32

Gnomad AFR AF: 0.594

Gnomad AMI AF: 0.803

Gnomad AMR AF: 0.659

Gnomad ASJ AF: 0.803

Gnomad EAS AF: 0.919

Gnomad SAS AF: 0.797

Gnomad FIN AF: 0.899

Gnomad MID AF: 0.744

Gnomad NFE AF: 0.791

Gnomad OTH AF: 0.737

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

GnomAD4 genome AF: 0.736 AC: 111921 AN: 152142 Hom.: 41967 Cov.: 32 AF XY: 0.740 AC XY: 55062 AN XY: 74384

African (AFR) AF: 0.594 AC: 24636 AN: 41472

American (AMR) AF: 0.659 AC: 10072 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.803 AC: 2782 AN: 3466

East Asian (EAS) AF: 0.918 AC: 4752 AN: 5174

South Asian (SAS) AF: 0.796 AC: 3838 AN: 4820

European-Finnish (FIN) AF: 0.899 AC: 9531 AN: 10600

Middle Eastern (MID) AF: 0.738 AC: 217 AN: 294

European-Non Finnish (NFE) AF: 0.791 AC: 53808 AN: 68004

Other (OTH) AF: 0.735 AC: 1553 AN: 2114

Alfa AF: 0.764 Hom.: 140250

Bravo AF: 0.711

Asia WGS AF: 0.844 AC: 2933 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	9.0
DANN	Benign	0.73
PhyloP100		0.34

Splicing

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

Other links and lift over

dbSNP: rs2148322; hg19: chr1-92122332;