rs1342852

Variant names:

• chr4-184384963-C-T
• rs1342852

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 0.349 in 151,906 control chromosomes in the GnomAD database, including 9,484 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 0.35 (9484 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0180
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.462 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: 0.349 AC: 53019 AN: 151788 Hom.: 9466 Cov.: 31

Gnomad AFR AF: 0.320

Gnomad AMI AF: 0.229

Gnomad AMR AF: 0.400

Gnomad ASJ AF: 0.345

Gnomad EAS AF: 0.297

Gnomad SAS AF: 0.478

Gnomad FIN AF: 0.296

Gnomad MID AF: 0.345

Gnomad NFE AF: 0.361

Gnomad OTH AF: 0.354

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

GnomAD4 genome AF: 0.349 AC: 53077 AN: 151906 Hom.: 9484 Cov.: 31 AF XY: 0.350 AC XY: 26007 AN XY: 74250

African (AFR) AF: 0.320 AC: 13258 AN: 41418

American (AMR) AF: 0.400 AC: 6113 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.345 AC: 1195 AN: 3464

East Asian (EAS) AF: 0.296 AC: 1533 AN: 5174

South Asian (SAS) AF: 0.479 AC: 2301 AN: 4808

European-Finnish (FIN) AF: 0.296 AC: 3125 AN: 10558

Middle Eastern (MID) AF: 0.347 AC: 102 AN: 294

European-Non Finnish (NFE) AF: 0.361 AC: 24495 AN: 67910

Other (OTH) AF: 0.355 AC: 747 AN: 2102

Alfa AF: 0.361 Hom.: 10226

Bravo AF: 0.355

Asia WGS AF: 0.385 AC: 1343 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	5.4
DANN	Benign	0.47
PhyloP100		0.018

Splicing

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

Other links and lift over

dbSNP: rs1342852; hg19: chr4-185306117;