4-110812980-T-C

Variant names:

• chr4-110812980-T-C
• rs3853444

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 0.288 in 151,668 control chromosomes in the GnomAD database, including 7,609 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 0.29 (7609 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.131
• Publications: 9 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.612 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: 0.288 AC: 43665 AN: 151550 Hom.: 7610 Cov.: 32

Gnomad AFR AF: 0.106

Gnomad AMI AF: 0.310

Gnomad AMR AF: 0.378

Gnomad ASJ AF: 0.267

Gnomad EAS AF: 0.632

Gnomad SAS AF: 0.423

Gnomad FIN AF: 0.377

Gnomad MID AF: 0.297

Gnomad NFE AF: 0.330

Gnomad OTH AF: 0.296

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

GnomAD4 genome AF: 0.288 AC: 43680 AN: 151668 Hom.: 7609 Cov.: 32 AF XY: 0.294 AC XY: 21766 AN XY: 74082

African (AFR) AF: 0.106 AC: 4413 AN: 41494

American (AMR) AF: 0.378 AC: 5733 AN: 15172

Ashkenazi Jewish (ASJ) AF: 0.267 AC: 923 AN: 3460

East Asian (EAS) AF: 0.630 AC: 3235 AN: 5132

South Asian (SAS) AF: 0.423 AC: 2036 AN: 4816

European-Finnish (FIN) AF: 0.377 AC: 3977 AN: 10542

Middle Eastern (MID) AF: 0.313 AC: 92 AN: 294

European-Non Finnish (NFE) AF: 0.330 AC: 22364 AN: 67740

Other (OTH) AF: 0.296 AC: 625 AN: 2108

Alfa AF: 0.312 Hom.: 10318

Bravo AF: 0.282

Asia WGS AF: 0.488 AC: 1693 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	1.9
DANN	Benign	0.48
PhyloP100		-0.13

Splicing

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

Other links and lift over

dbSNP: rs3853444; hg19: chr4-111734136; COSMIC: COSV53894420;