chr1-24977085-A-G

Variant names:

• chr1-24977085-A-G
• rs10903122

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 0.563 in 152,052 control chromosomes in the GnomAD database, including 24,519 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 0.56 (24519 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.93
• Publications: 43 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.68 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: 0.563 AC: 85526 AN: 151934 Hom.: 24477 Cov.: 32

Gnomad AFR AF: 0.592

Gnomad AMI AF: 0.690

Gnomad AMR AF: 0.673

Gnomad ASJ AF: 0.529

Gnomad EAS AF: 0.699

Gnomad SAS AF: 0.680

Gnomad FIN AF: 0.561

Gnomad MID AF: 0.544

Gnomad NFE AF: 0.502

Gnomad OTH AF: 0.578

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

GnomAD4 genome AF: 0.563 AC: 85611 AN: 152052 Hom.: 24519 Cov.: 32 AF XY: 0.574 AC XY: 42691 AN XY: 74324

African (AFR) AF: 0.592 AC: 24523 AN: 41454

American (AMR) AF: 0.674 AC: 10296 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.529 AC: 1835 AN: 3472

East Asian (EAS) AF: 0.699 AC: 3616 AN: 5174

South Asian (SAS) AF: 0.679 AC: 3272 AN: 4816

European-Finnish (FIN) AF: 0.561 AC: 5916 AN: 10542

Middle Eastern (MID) AF: 0.551 AC: 162 AN: 294

European-Non Finnish (NFE) AF: 0.502 AC: 34133 AN: 67994

Other (OTH) AF: 0.582 AC: 1229 AN: 2110

Alfa AF: 0.522 Hom.: 72060

Bravo AF: 0.574

Asia WGS AF: 0.707 AC: 2459 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	6.9
DANN	Benign	0.62
PhyloP100		1.9

Splicing

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

Other links and lift over

dbSNP: rs10903122; hg19: chr1-25303576;