rs340191

chr4-85418337-T-A

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 0.342 in 152,032 control chromosomes in the GnomAD database, including 9,309 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 0.34 (9309 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.03

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.391 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.342 AC: 51965 AN: 151914 Hom.: 9294 Cov.: 31

Gnomad AFR AF: 0.269

Gnomad AMI AF: 0.348

Gnomad AMR AF: 0.367

Gnomad ASJ AF: 0.341

Gnomad EAS AF: 0.231

Gnomad SAS AF: 0.181

Gnomad FIN AF: 0.375

Gnomad MID AF: 0.366

Gnomad NFE AF: 0.395

Gnomad OTH AF: 0.363

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

GnomAD4 genome AF: 0.342 AC: 52020 AN: 152032 Hom.: 9309 Cov.: 31 AF XY: 0.338 AC XY: 25131 AN XY: 74310

Gnomad4 AFR AF: 0.270

Gnomad4 AMR AF: 0.368

Gnomad4 ASJ AF: 0.341

Gnomad4 EAS AF: 0.231

Gnomad4 SAS AF: 0.180

Gnomad4 FIN AF: 0.375

Gnomad4 NFE AF: 0.395

Gnomad4 OTH AF: 0.360

Alfa AF: 0.369 Hom.: 1318

Bravo AF: 0.343

Asia WGS AF: 0.221 AC: 769 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	0.11
Dann	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs340191; hg19: chr4-86339490;