rs1159918

Variant names:

• chr4-99321852-A-C
• rs1159918

Your query was ambiguous. Multiple possible variants found:

• chr4-99321852-A-C
• chr4-99321852-A-G
• chr4-99321852-A-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 0.536 in 151,934 control chromosomes in the GnomAD database, including 23,924 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 0.54 (23924 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.122
• Publications: 34 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.803 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: 0.536 AC: 81439 AN: 151816 Hom.: 23930 Cov.: 31

Gnomad AFR AF: 0.301

Gnomad AMI AF: 0.806

Gnomad AMR AF: 0.461

Gnomad ASJ AF: 0.691

Gnomad EAS AF: 0.823

Gnomad SAS AF: 0.633

Gnomad FIN AF: 0.553

Gnomad MID AF: 0.655

Gnomad NFE AF: 0.652

Gnomad OTH AF: 0.575

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

GnomAD4 genome AF: 0.536 AC: 81443 AN: 151934 Hom.: 23924 Cov.: 31 AF XY: 0.532 AC XY: 39529 AN XY: 74258

African (AFR) AF: 0.301 AC: 12469 AN: 41434

American (AMR) AF: 0.460 AC: 7022 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.691 AC: 2399 AN: 3472

East Asian (EAS) AF: 0.823 AC: 4240 AN: 5150

South Asian (SAS) AF: 0.633 AC: 3038 AN: 4802

European-Finnish (FIN) AF: 0.553 AC: 5837 AN: 10560

Middle Eastern (MID) AF: 0.650 AC: 191 AN: 294

European-Non Finnish (NFE) AF: 0.652 AC: 44310 AN: 67936

Other (OTH) AF: 0.571 AC: 1202 AN: 2104

Alfa AF: 0.609 Hom.: 88389

Bravo AF: 0.516

Asia WGS AF: 0.582 AC: 2024 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.4
DANN	Benign	0.50
PhyloP100		-0.12
PromoterAI		-0.12	Neutral

Splicing

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

Other links and lift over

dbSNP: rs1159918; hg19: chr4-100243009;