rs790146

Variant names:

• chr4-40721541-T-C
• rs790146

Your query was ambiguous. Multiple possible variants found:

• chr4-40721541-T-C
• chr4-40721541-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 0.284 in 140,632 control chromosomes in the GnomAD database, including 6,203 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 0.28 (6203 hom., cov: 21)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.703
• Publications: 2 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 = 0.435 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: 0.284 AC: 39960 AN: 140570 Hom.: 6195 Cov.: 21

Gnomad AFR AF: 0.183

Gnomad AMI AF: 0.434

Gnomad AMR AF: 0.407

Gnomad ASJ AF: 0.348

Gnomad EAS AF: 0.450

Gnomad SAS AF: 0.221

Gnomad FIN AF: 0.214

Gnomad MID AF: 0.303

Gnomad NFE AF: 0.311

Gnomad OTH AF: 0.287

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

GnomAD4 genome AF: 0.284 AC: 39978 AN: 140632 Hom.: 6203 Cov.: 21 AF XY: 0.280 AC XY: 18977 AN XY: 67784

African (AFR) AF: 0.183 AC: 6748 AN: 36916

American (AMR) AF: 0.408 AC: 5614 AN: 13770

Ashkenazi Jewish (ASJ) AF: 0.348 AC: 1186 AN: 3408

East Asian (EAS) AF: 0.451 AC: 2181 AN: 4834

South Asian (SAS) AF: 0.221 AC: 967 AN: 4378

European-Finnish (FIN) AF: 0.214 AC: 1783 AN: 8340

Middle Eastern (MID) AF: 0.294 AC: 80 AN: 272

European-Non Finnish (NFE) AF: 0.311 AC: 20495 AN: 65940

Other (OTH) AF: 0.287 AC: 547 AN: 1906

Alfa AF: 0.280 Hom.: 825

Bravo AF: 0.294

Asia WGS AF: 0.298 AC: 1036 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	4.1
DANN	Benign	0.65
PhyloP100		-0.70

Splicing

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

Other links and lift over

dbSNP: rs790146; hg19: chr4-40723558; COSMIC: COSV50509966;