chr1-91454053-A-G

Variant names:

• chr1-91454053-A-G
• rs17131455

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 0.0414 in 152,290 control chromosomes in the GnomAD database, including 210 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 0.041 (210 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.574
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0953 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: 0.0413 AC: 6292 AN: 152172 Hom.: 210 Cov.: 32

Gnomad AFR AF: 0.0803

Gnomad AMI AF: 0.0242

Gnomad AMR AF: 0.0219

Gnomad ASJ AF: 0.0127

Gnomad EAS AF: 0.0294

Gnomad SAS AF: 0.103

Gnomad FIN AF: 0.00904

Gnomad MID AF: 0.0823

Gnomad NFE AF: 0.0250

Gnomad OTH AF: 0.0421

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

GnomAD4 genome AF: 0.0414 AC: 6305 AN: 152290 Hom.: 210 Cov.: 32 AF XY: 0.0411 AC XY: 3060 AN XY: 74478

African (AFR) AF: 0.0804 AC: 3339 AN: 41548

American (AMR) AF: 0.0218 AC: 334 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.0127 AC: 44 AN: 3472

East Asian (EAS) AF: 0.0293 AC: 152 AN: 5186

South Asian (SAS) AF: 0.103 AC: 496 AN: 4828

European-Finnish (FIN) AF: 0.00904 AC: 96 AN: 10618

Middle Eastern (MID) AF: 0.0850 AC: 25 AN: 294

European-Non Finnish (NFE) AF: 0.0251 AC: 1705 AN: 68016

Other (OTH) AF: 0.0435 AC: 92 AN: 2114

Alfa AF: 0.0307 Hom.: 124

Bravo AF: 0.0414

Asia WGS AF: 0.0700 AC: 245 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	5.2
DANN	Benign	0.83
PhyloP100		-0.57

Splicing

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

Other links and lift over

dbSNP: rs17131455; hg19: chr1-91919610;