4-100885375-C-G

Variant names:

• chr4-100885375-C-G
• rs13107740

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 0.217 in 151,270 control chromosomes in the GnomAD database, including 3,759 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 0.22 (3759 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.52
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.246 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: 0.217 AC: 32804 AN: 151152 Hom.: 3748 Cov.: 32

Gnomad AFR AF: 0.173

Gnomad AMI AF: 0.196

Gnomad AMR AF: 0.218

Gnomad ASJ AF: 0.216

Gnomad EAS AF: 0.103

Gnomad SAS AF: 0.213

Gnomad FIN AF: 0.254

Gnomad MID AF: 0.168

Gnomad NFE AF: 0.249

Gnomad OTH AF: 0.178

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

GnomAD4 genome AF: 0.217 AC: 32851 AN: 151270 Hom.: 3759 Cov.: 32 AF XY: 0.219 AC XY: 16175 AN XY: 73912

African (AFR) AF: 0.173 AC: 7174 AN: 41378

American (AMR) AF: 0.217 AC: 3297 AN: 15166

Ashkenazi Jewish (ASJ) AF: 0.216 AC: 745 AN: 3454

East Asian (EAS) AF: 0.103 AC: 531 AN: 5166

South Asian (SAS) AF: 0.215 AC: 1034 AN: 4814

European-Finnish (FIN) AF: 0.254 AC: 2681 AN: 10536

Middle Eastern (MID) AF: 0.163 AC: 48 AN: 294

European-Non Finnish (NFE) AF: 0.249 AC: 16780 AN: 67452

Other (OTH) AF: 0.182 AC: 383 AN: 2100

Alfa AF: 0.131 Hom.: 256

Bravo AF: 0.211

Asia WGS AF: 0.198 AC: 687 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.088
DANN	Benign	0.59
PhyloP100		-3.5

Splicing

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

Other links and lift over

dbSNP: rs13107740; hg19: chr4-101806532;