4-99374258-T-C

Variant names:

• chr4-99374258-T-C
• rs1121534

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 0.25 in 152,008 control chromosomes in the GnomAD database, including 5,552 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 0.25 (5552 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.50
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.657 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: 0.250 AC: 37970 AN: 151890 Hom.: 5545 Cov.: 32

Gnomad AFR AF: 0.307

Gnomad AMI AF: 0.254

Gnomad AMR AF: 0.183

Gnomad ASJ AF: 0.175

Gnomad EAS AF: 0.675

Gnomad SAS AF: 0.467

Gnomad FIN AF: 0.172

Gnomad MID AF: 0.209

Gnomad NFE AF: 0.199

Gnomad OTH AF: 0.239

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

GnomAD4 genome AF: 0.250 AC: 38004 AN: 152008 Hom.: 5552 Cov.: 32 AF XY: 0.257 AC XY: 19100 AN XY: 74320

African (AFR) AF: 0.307 AC: 12729 AN: 41432

American (AMR) AF: 0.183 AC: 2798 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.175 AC: 608 AN: 3470

East Asian (EAS) AF: 0.676 AC: 3487 AN: 5160

South Asian (SAS) AF: 0.466 AC: 2242 AN: 4810

European-Finnish (FIN) AF: 0.172 AC: 1817 AN: 10564

Middle Eastern (MID) AF: 0.211 AC: 62 AN: 294

European-Non Finnish (NFE) AF: 0.199 AC: 13528 AN: 67980

Other (OTH) AF: 0.237 AC: 501 AN: 2110

Alfa AF: 0.212 Hom.: 1639

Bravo AF: 0.250

Asia WGS AF: 0.469 AC: 1628 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	3.3
DANN	Benign	0.63
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs1121534; hg19: chr4-100295415;