rs3811791

Variant names:

• chr4-140570619-T-C
• rs3811791

Your query was ambiguous. Multiple possible variants found:

• chr4-140570619-T-C
• chr4-140570619-T-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.0689 in 152,174 control chromosomes in the GnomAD database, including 980 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 0.069 (980 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.114

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.73).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.236 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: 0.0687 AC: 10453 AN: 152056 Hom.: 977 Cov.: 32

Gnomad AFR AF: 0.192

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0376

Gnomad ASJ AF: 0.0167

Gnomad EAS AF: 0.248

Gnomad SAS AF: 0.0595

Gnomad FIN AF: 0.0000942

Gnomad MID AF: 0.0190

Gnomad NFE AF: 0.00288

Gnomad OTH AF: 0.0531

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

GnomAD4 genome AF: 0.0689 AC: 10486 AN: 152174 Hom.: 980 Cov.: 32 AF XY: 0.0696 AC XY: 5183 AN XY: 74420

Gnomad4 AFR AF: 0.192

Gnomad4 AMR AF: 0.0375

Gnomad4 ASJ AF: 0.0167

Gnomad4 EAS AF: 0.247

Gnomad4 SAS AF: 0.0600

Gnomad4 FIN AF: 0.0000942

Gnomad4 NFE AF: 0.00287

Gnomad4 OTH AF: 0.0563

Alfa AF: 0.0428 Hom.: 142

Bravo AF: 0.0774

Asia WGS AF: 0.143 AC: 498 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.73
CADD	Benign	7.5
DANN	Benign	0.89

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3811791; hg19: chr4-141491773;