rs924134

Variant names:

• chr5-2468261-C-A
• rs924134

Your query was ambiguous. Multiple possible variants found:

• chr5-2468261-C-A
• chr5-2468261-C-G
• chr5-2468261-C-T

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 0.521 in 152,044 control chromosomes in the GnomAD database, including 23,054 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 0.52 (23054 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.45
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.788 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: 0.521 AC: 79099 AN: 151926 Hom.: 22997 Cov.: 33

Gnomad AFR AF: 0.795

Gnomad AMI AF: 0.443

Gnomad AMR AF: 0.465

Gnomad ASJ AF: 0.422

Gnomad EAS AF: 0.559

Gnomad SAS AF: 0.535

Gnomad FIN AF: 0.394

Gnomad MID AF: 0.436

Gnomad NFE AF: 0.390

Gnomad OTH AF: 0.472

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

GnomAD4 genome AF: 0.521 AC: 79232 AN: 152044 Hom.: 23054 Cov.: 33 AF XY: 0.523 AC XY: 38835 AN XY: 74322

African (AFR) AF: 0.796 AC: 33002 AN: 41480

American (AMR) AF: 0.465 AC: 7107 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.422 AC: 1463 AN: 3468

East Asian (EAS) AF: 0.560 AC: 2887 AN: 5158

South Asian (SAS) AF: 0.536 AC: 2579 AN: 4814

European-Finnish (FIN) AF: 0.394 AC: 4168 AN: 10566

Middle Eastern (MID) AF: 0.435 AC: 127 AN: 292

European-Non Finnish (NFE) AF: 0.390 AC: 26494 AN: 67968

Other (OTH) AF: 0.475 AC: 1001 AN: 2106

Alfa AF: 0.427 Hom.: 56450

Bravo AF: 0.533

Asia WGS AF: 0.569 AC: 1978 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.032
DANN	Benign	0.45
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs924134; hg19: chr5-2468375;