4-104454266-T-G

Variant names:

• chr4-104454266-T-G
• rs7657799

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 0.218 in 152,232 control chromosomes in the GnomAD database, including 10,373 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 (10373 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.190
• Publications: 14 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.687 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: 0.218 AC: 33157 AN: 152112 Hom.: 10336 Cov.: 32

Gnomad AFR AF: 0.693

Gnomad AMI AF: 0.00987

Gnomad AMR AF: 0.0866

Gnomad ASJ AF: 0.0455

Gnomad EAS AF: 0.167

Gnomad SAS AF: 0.0655

Gnomad FIN AF: 0.00452

Gnomad MID AF: 0.0701

Gnomad NFE AF: 0.0204

Gnomad OTH AF: 0.164

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

GnomAD4 genome AF: 0.218 AC: 33245 AN: 152232 Hom.: 10373 Cov.: 32 AF XY: 0.214 AC XY: 15913 AN XY: 74448

African (AFR) AF: 0.693 AC: 28773 AN: 41494

American (AMR) AF: 0.0864 AC: 1321 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0455 AC: 158 AN: 3472

East Asian (EAS) AF: 0.166 AC: 859 AN: 5182

South Asian (SAS) AF: 0.0665 AC: 321 AN: 4824

European-Finnish (FIN) AF: 0.00452 AC: 48 AN: 10624

Middle Eastern (MID) AF: 0.0748 AC: 22 AN: 294

European-Non Finnish (NFE) AF: 0.0204 AC: 1391 AN: 68022

Other (OTH) AF: 0.162 AC: 343 AN: 2112

Alfa AF: 0.0841 Hom.: 10386

Bravo AF: 0.246

Asia WGS AF: 0.150 AC: 522 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.89
DANN	Benign	0.75
PhyloP100		-0.19

Splicing

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

Other links and lift over

dbSNP: rs7657799; hg19: chr4-105375423;