4-102099647-T-C

Variant names:

• chr4-102099647-T-C
• rs238486

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 0.426 in 151,984 control chromosomes in the GnomAD database, including 13,990 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 0.43 (13990 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.544
• Publications: 5 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 (AFR) allele frequency at 95% confidence interval = 0.44 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: 0.426 AC: 64623 AN: 151866 Hom.: 13965 Cov.: 32

Gnomad AFR AF: 0.446

Gnomad AMI AF: 0.322

Gnomad AMR AF: 0.367

Gnomad ASJ AF: 0.375

Gnomad EAS AF: 0.349

Gnomad SAS AF: 0.383

Gnomad FIN AF: 0.548

Gnomad MID AF: 0.396

Gnomad NFE AF: 0.422

Gnomad OTH AF: 0.386

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

GnomAD4 genome AF: 0.426 AC: 64691 AN: 151984 Hom.: 13990 Cov.: 32 AF XY: 0.429 AC XY: 31898 AN XY: 74280

African (AFR) AF: 0.446 AC: 18473 AN: 41440

American (AMR) AF: 0.368 AC: 5612 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.375 AC: 1300 AN: 3468

East Asian (EAS) AF: 0.349 AC: 1806 AN: 5176

South Asian (SAS) AF: 0.383 AC: 1848 AN: 4828

European-Finnish (FIN) AF: 0.548 AC: 5772 AN: 10524

Middle Eastern (MID) AF: 0.388 AC: 114 AN: 294

European-Non Finnish (NFE) AF: 0.422 AC: 28661 AN: 67972

Other (OTH) AF: 0.385 AC: 813 AN: 2112

Alfa AF: 0.421 Hom.: 2384

Bravo AF: 0.412

Asia WGS AF: 0.359 AC: 1245 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	4.3
DANN	Benign	0.78
PhyloP100		0.54

Splicing

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

Other links and lift over

dbSNP: rs238486; hg19: chr4-103020804;