4-103738447-C-T

Variant names:

• chr4-103738447-C-T
• rs17034046

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 0.34 in 149,346 control chromosomes in the GnomAD database, including 13,150 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 (13150 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.50
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.72 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: 0.340 AC: 50687 AN: 149236 Hom.: 13108 Cov.: 31

Gnomad AFR AF: 0.727

Gnomad AMI AF: 0.206

Gnomad AMR AF: 0.248

Gnomad ASJ AF: 0.173

Gnomad EAS AF: 0.361

Gnomad SAS AF: 0.338

Gnomad FIN AF: 0.195

Gnomad MID AF: 0.192

Gnomad NFE AF: 0.155

Gnomad OTH AF: 0.308

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

GnomAD4 genome AF: 0.340 AC: 50785 AN: 149346 Hom.: 13150 Cov.: 31 AF XY: 0.341 AC XY: 24778 AN XY: 72588

African (AFR) AF: 0.727 AC: 29936 AN: 41172

American (AMR) AF: 0.248 AC: 3698 AN: 14920

Ashkenazi Jewish (ASJ) AF: 0.173 AC: 595 AN: 3444

East Asian (EAS) AF: 0.361 AC: 1836 AN: 5082

South Asian (SAS) AF: 0.338 AC: 1606 AN: 4758

European-Finnish (FIN) AF: 0.195 AC: 1849 AN: 9488

Middle Eastern (MID) AF: 0.181 AC: 52 AN: 288

European-Non Finnish (NFE) AF: 0.155 AC: 10387 AN: 67210

Other (OTH) AF: 0.308 AC: 641 AN: 2084

Alfa AF: 0.232 Hom.: 846

Bravo AF: 0.355

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.063
DANN	Benign	0.56
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs17034046; hg19: chr4-104659604;