chr4-109911150-T-C

Variant names:

• chr4-109911150-T-C
• rs3756261

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 0.0991 in 152,142 control chromosomes in the GnomAD database, including 1,087 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 0.099 (1087 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.505
• Publications: 15 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.192 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: 0.0989 AC: 15039 AN: 152024 Hom.: 1082 Cov.: 32

Gnomad AFR AF: 0.183

Gnomad AMI AF: 0.164

Gnomad AMR AF: 0.0941

Gnomad ASJ AF: 0.0839

Gnomad EAS AF: 0.203

Gnomad SAS AF: 0.0834

Gnomad FIN AF: 0.0427

Gnomad MID AF: 0.0475

Gnomad NFE AF: 0.0514

Gnomad OTH AF: 0.0908

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

GnomAD4 genome AF: 0.0991 AC: 15076 AN: 152142 Hom.: 1087 Cov.: 32 AF XY: 0.101 AC XY: 7482 AN XY: 74402

African (AFR) AF: 0.183 AC: 7587 AN: 41472

American (AMR) AF: 0.0938 AC: 1433 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.0839 AC: 291 AN: 3470

East Asian (EAS) AF: 0.202 AC: 1046 AN: 5172

South Asian (SAS) AF: 0.0841 AC: 405 AN: 4814

European-Finnish (FIN) AF: 0.0427 AC: 453 AN: 10614

Middle Eastern (MID) AF: 0.0476 AC: 14 AN: 294

European-Non Finnish (NFE) AF: 0.0515 AC: 3500 AN: 68000

Other (OTH) AF: 0.0937 AC: 198 AN: 2114

Alfa AF: 0.0796 Hom.: 194

Bravo AF: 0.107

Asia WGS AF: 0.133 AC: 463 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.0
DANN	Benign	0.40
PhyloP100		-0.51

Splicing

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

Other links and lift over

dbSNP: rs3756261; hg19: chr4-110832306;