rs910112

Variant names:

• chr1-54460108-C-T
• rs910112

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 0.165 in 152,054 control chromosomes in the GnomAD database, including 3,641 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 0.17 (3641 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0980
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.386 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: 0.165 AC: 25073 AN: 151936 Hom.: 3633 Cov.: 32

Gnomad AFR AF: 0.391

Gnomad AMI AF: 0.00987

Gnomad AMR AF: 0.103

Gnomad ASJ AF: 0.0928

Gnomad EAS AF: 0.141

Gnomad SAS AF: 0.134

Gnomad FIN AF: 0.138

Gnomad MID AF: 0.196

Gnomad NFE AF: 0.0566

Gnomad OTH AF: 0.132

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

GnomAD4 genome AF: 0.165 AC: 25128 AN: 152054 Hom.: 3641 Cov.: 32 AF XY: 0.167 AC XY: 12377 AN XY: 74314

African (AFR) AF: 0.391 AC: 16188 AN: 41416

American (AMR) AF: 0.103 AC: 1578 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.0928 AC: 322 AN: 3470

East Asian (EAS) AF: 0.141 AC: 728 AN: 5168

South Asian (SAS) AF: 0.134 AC: 648 AN: 4824

European-Finnish (FIN) AF: 0.138 AC: 1458 AN: 10596

Middle Eastern (MID) AF: 0.204 AC: 60 AN: 294

European-Non Finnish (NFE) AF: 0.0566 AC: 3851 AN: 67988

Other (OTH) AF: 0.135 AC: 286 AN: 2112

Alfa AF: 0.129 Hom.: 419

Bravo AF: 0.173

Asia WGS AF: 0.164 AC: 568 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.1
DANN	Benign	0.45
PhyloP100		0.098

Splicing

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

Other links and lift over

dbSNP: rs910112; hg19: chr1-54925781;