rs2123315

Variant names:

• chr4-18964946-T-C
• rs2123315

Your query was ambiguous. Multiple possible variants found:

• chr4-18964946-T-C
• chr4-18964946-T-G

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 0.117 in 151,996 control chromosomes in the GnomAD database, including 1,728 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 0.12 (1728 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.326
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.263 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: 0.116 AC: 17671 AN: 151878 Hom.: 1716 Cov.: 32

Gnomad AFR AF: 0.267

Gnomad AMI AF: 0.0219

Gnomad AMR AF: 0.0701

Gnomad ASJ AF: 0.0590

Gnomad EAS AF: 0.0430

Gnomad SAS AF: 0.153

Gnomad FIN AF: 0.0267

Gnomad MID AF: 0.133

Gnomad NFE AF: 0.0559

Gnomad OTH AF: 0.121

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

GnomAD4 genome AF: 0.117 AC: 17713 AN: 151996 Hom.: 1728 Cov.: 32 AF XY: 0.115 AC XY: 8540 AN XY: 74294

African (AFR) AF: 0.268 AC: 11089 AN: 41448

American (AMR) AF: 0.0699 AC: 1066 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.0590 AC: 205 AN: 3472

East Asian (EAS) AF: 0.0433 AC: 224 AN: 5170

South Asian (SAS) AF: 0.152 AC: 733 AN: 4818

European-Finnish (FIN) AF: 0.0267 AC: 283 AN: 10592

Middle Eastern (MID) AF: 0.136 AC: 40 AN: 294

European-Non Finnish (NFE) AF: 0.0559 AC: 3800 AN: 67942

Other (OTH) AF: 0.120 AC: 253 AN: 2102

Alfa AF: 0.0240 Hom.: 17

Bravo AF: 0.124

Asia WGS AF: 0.0960 AC: 338 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.7
DANN	Benign	0.71
PhyloP100		-0.33

Splicing

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

Other links and lift over

dbSNP: rs2123315; hg19: chr4-18966569;