rs3974759

Variant names:

• chr18-11979295-T-A
• rs3974759

Your query was ambiguous. Multiple possible variants found:

• chr18-11979295-T-A
• chr18-11979295-T-C
• chr18-11979295-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 0.449 in 152,036 control chromosomes in the GnomAD database, including 18,594 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 0.45 (18594 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.426
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.738 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: 0.448 AC: 68103 AN: 151918 Hom.: 18536 Cov.: 32

Gnomad AFR AF: 0.744

Gnomad AMI AF: 0.378

Gnomad AMR AF: 0.424

Gnomad ASJ AF: 0.271

Gnomad EAS AF: 0.684

Gnomad SAS AF: 0.510

Gnomad FIN AF: 0.289

Gnomad MID AF: 0.418

Gnomad NFE AF: 0.287

Gnomad OTH AF: 0.409

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

GnomAD4 genome AF: 0.449 AC: 68217 AN: 152036 Hom.: 18594 Cov.: 32 AF XY: 0.451 AC XY: 33496 AN XY: 74324

African (AFR) AF: 0.745 AC: 30885 AN: 41478

American (AMR) AF: 0.425 AC: 6484 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.271 AC: 939 AN: 3468

East Asian (EAS) AF: 0.684 AC: 3537 AN: 5174

South Asian (SAS) AF: 0.510 AC: 2460 AN: 4826

European-Finnish (FIN) AF: 0.289 AC: 3053 AN: 10556

Middle Eastern (MID) AF: 0.405 AC: 119 AN: 294

European-Non Finnish (NFE) AF: 0.287 AC: 19531 AN: 67958

Other (OTH) AF: 0.412 AC: 865 AN: 2102

Alfa AF: 0.381 Hom.: 1632

Bravo AF: 0.471

Asia WGS AF: 0.604 AC: 2096 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.5
DANN	Benign	0.74
PhyloP100		-0.43

Splicing

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

Other links and lift over

dbSNP: rs3974759; hg19: chr18-11979294;