4-34923442-A-G

Variant names:

• chr4-34923442-A-G
• rs1317830

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 0.336 in 151,938 control chromosomes in the GnomAD database, including 8,777 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 (8777 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.247
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.421 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: 0.336 AC: 51036 AN: 151820 Hom.: 8765 Cov.: 31

Gnomad AFR AF: 0.426

Gnomad AMI AF: 0.421

Gnomad AMR AF: 0.296

Gnomad ASJ AF: 0.328

Gnomad EAS AF: 0.293

Gnomad SAS AF: 0.333

Gnomad FIN AF: 0.255

Gnomad MID AF: 0.437

Gnomad NFE AF: 0.305

Gnomad OTH AF: 0.346

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

GnomAD4 genome AF: 0.336 AC: 51093 AN: 151938 Hom.: 8777 Cov.: 31 AF XY: 0.333 AC XY: 24756 AN XY: 74240

African (AFR) AF: 0.426 AC: 17671 AN: 41444

American (AMR) AF: 0.296 AC: 4512 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.328 AC: 1138 AN: 3468

East Asian (EAS) AF: 0.293 AC: 1504 AN: 5130

South Asian (SAS) AF: 0.335 AC: 1610 AN: 4812

European-Finnish (FIN) AF: 0.255 AC: 2689 AN: 10564

Middle Eastern (MID) AF: 0.425 AC: 125 AN: 294

European-Non Finnish (NFE) AF: 0.305 AC: 20735 AN: 67964

Other (OTH) AF: 0.346 AC: 727 AN: 2104

Alfa AF: 0.330 Hom.: 7205

Bravo AF: 0.344

Asia WGS AF: 0.303 AC: 1059 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	2.1
DANN	Benign	0.32
PhyloP100		-0.25

Splicing

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

Other links and lift over

dbSNP: rs1317830; hg19: chr4-34925064;