4-110780642-G-T

Variant names:

• chr4-110780642-G-T
• rs1906615

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 0.285 in 151,876 control chromosomes in the GnomAD database, including 7,114 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 (7114 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.07
• Publications: 9 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.71 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: 0.285 AC: 43300 AN: 151758 Hom.: 7106 Cov.: 32

Gnomad AFR AF: 0.290

Gnomad AMI AF: 0.0769

Gnomad AMR AF: 0.393

Gnomad ASJ AF: 0.379

Gnomad EAS AF: 0.729

Gnomad SAS AF: 0.336

Gnomad FIN AF: 0.232

Gnomad MID AF: 0.297

Gnomad NFE AF: 0.227

Gnomad OTH AF: 0.283

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

GnomAD4 genome AF: 0.285 AC: 43321 AN: 151876 Hom.: 7114 Cov.: 32 AF XY: 0.297 AC XY: 22068 AN XY: 74218

African (AFR) AF: 0.290 AC: 11994 AN: 41420

American (AMR) AF: 0.393 AC: 5997 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.379 AC: 1315 AN: 3466

East Asian (EAS) AF: 0.730 AC: 3762 AN: 5156

South Asian (SAS) AF: 0.335 AC: 1612 AN: 4808

European-Finnish (FIN) AF: 0.232 AC: 2435 AN: 10516

Middle Eastern (MID) AF: 0.299 AC: 88 AN: 294

European-Non Finnish (NFE) AF: 0.227 AC: 15454 AN: 67950

Other (OTH) AF: 0.282 AC: 594 AN: 2106

Alfa AF: 0.256 Hom.: 1690

Bravo AF: 0.294

Asia WGS AF: 0.474 AC: 1647 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	3.3
DANN	Benign	0.68
PhyloP100		1.1

Splicing

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

Other links and lift over

dbSNP: rs1906615; hg19: chr4-111701798;