rs10922323

Variant names:

• chr1-197893191-T-C
• rs10922323

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 0.427 in 152,010 control chromosomes in the GnomAD database, including 14,069 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 0.43 (14069 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.18
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.494 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: 0.427 AC: 64920 AN: 151892 Hom.: 14050 Cov.: 32

Gnomad AFR AF: 0.500

Gnomad AMI AF: 0.555

Gnomad AMR AF: 0.370

Gnomad ASJ AF: 0.458

Gnomad EAS AF: 0.337

Gnomad SAS AF: 0.457

Gnomad FIN AF: 0.366

Gnomad MID AF: 0.538

Gnomad NFE AF: 0.407

Gnomad OTH AF: 0.423

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

GnomAD4 genome AF: 0.427 AC: 64973 AN: 152010 Hom.: 14069 Cov.: 32 AF XY: 0.423 AC XY: 31400 AN XY: 74304

African (AFR) AF: 0.500 AC: 20724 AN: 41444

American (AMR) AF: 0.370 AC: 5657 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.458 AC: 1587 AN: 3464

East Asian (EAS) AF: 0.337 AC: 1741 AN: 5172

South Asian (SAS) AF: 0.457 AC: 2198 AN: 4814

European-Finnish (FIN) AF: 0.366 AC: 3868 AN: 10562

Middle Eastern (MID) AF: 0.555 AC: 162 AN: 292

European-Non Finnish (NFE) AF: 0.407 AC: 27633 AN: 67950

Other (OTH) AF: 0.426 AC: 899 AN: 2110

Alfa AF: 0.415 Hom.: 22106

Bravo AF: 0.429

Asia WGS AF: 0.426 AC: 1484 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	5.4
DANN	Benign	0.84
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs10922323; hg19: chr1-197862321;