rs1317830

Positions:

• chr4-34923442-A-G
• chr4-34923442-A-T

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 0.336 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

Gnomad4 AFR AF: 0.426

Gnomad4 AMR AF: 0.296

Gnomad4 ASJ AF: 0.328

Gnomad4 EAS AF: 0.293

Gnomad4 SAS AF: 0.335

Gnomad4 FIN AF: 0.255

Gnomad4 NFE AF: 0.305

Gnomad4 OTH AF: 0.346

Alfa AF: 0.316 Hom.: 4232

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1317830; hg19: chr4-34925064;