4-34798278-C-T

Variant names:

• chr4-34798278-C-T
• rs7689126

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 0.304 in 138,314 control chromosomes in the GnomAD database, including 15,862 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 0.30 (15862 hom., cov: 24)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.03
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.05).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.804 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: 0.303 AC: 41930 AN: 138210 Hom.: 15819 Cov.: 24

Gnomad AFR AF: 0.811

Gnomad AMI AF: 0.0146

Gnomad AMR AF: 0.194

Gnomad ASJ AF: 0.0894

Gnomad EAS AF: 0.165

Gnomad SAS AF: 0.202

Gnomad FIN AF: 0.0558

Gnomad MID AF: 0.170

Gnomad NFE AF: 0.0789

Gnomad OTH AF: 0.264

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

GnomAD4 genome AF: 0.304 AC: 42032 AN: 138314 Hom.: 15862 Cov.: 24 AF XY: 0.296 AC XY: 19958 AN XY: 67378

African (AFR) AF: 0.811 AC: 31449 AN: 38758

American (AMR) AF: 0.194 AC: 2691 AN: 13900

Ashkenazi Jewish (ASJ) AF: 0.0894 AC: 284 AN: 3176

East Asian (EAS) AF: 0.164 AC: 821 AN: 4994

South Asian (SAS) AF: 0.202 AC: 902 AN: 4460

European-Finnish (FIN) AF: 0.0558 AC: 494 AN: 8860

Middle Eastern (MID) AF: 0.178 AC: 46 AN: 258

European-Non Finnish (NFE) AF: 0.0789 AC: 4835 AN: 61276

Other (OTH) AF: 0.265 AC: 499 AN: 1880

Alfa AF: 0.0660 Hom.: 231

Asia WGS AF: 0.207 AC: 702 AN: 3376

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.95
DANN	Benign	0.49
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs7689126; hg19: chr4-34799900;