4-102078452-T-C

Variant names:

• chr4-102078452-T-C
• rs6816285

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 0.61 in 152,026 control chromosomes in the GnomAD database, including 28,717 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 0.61 (28717 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.538
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.671 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: 0.610 AC: 92637 AN: 151908 Hom.: 28687 Cov.: 31

Gnomad AFR AF: 0.678

Gnomad AMI AF: 0.669

Gnomad AMR AF: 0.646

Gnomad ASJ AF: 0.624

Gnomad EAS AF: 0.666

Gnomad SAS AF: 0.621

Gnomad FIN AF: 0.451

Gnomad MID AF: 0.576

Gnomad NFE AF: 0.578

Gnomad OTH AF: 0.637

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

GnomAD4 genome AF: 0.610 AC: 92712 AN: 152026 Hom.: 28717 Cov.: 31 AF XY: 0.603 AC XY: 44818 AN XY: 74314

African (AFR) AF: 0.678 AC: 28097 AN: 41452

American (AMR) AF: 0.645 AC: 9858 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.624 AC: 2167 AN: 3470

East Asian (EAS) AF: 0.666 AC: 3441 AN: 5166

South Asian (SAS) AF: 0.620 AC: 2982 AN: 4808

European-Finnish (FIN) AF: 0.451 AC: 4754 AN: 10548

Middle Eastern (MID) AF: 0.582 AC: 170 AN: 292

European-Non Finnish (NFE) AF: 0.578 AC: 39285 AN: 67982

Other (OTH) AF: 0.638 AC: 1348 AN: 2112

Alfa AF: 0.583 Hom.: 3292

Bravo AF: 0.628

Asia WGS AF: 0.665 AC: 2315 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	9.2
DANN	Benign	0.49
PhyloP100		-0.54

Splicing

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

Other links and lift over

dbSNP: rs6816285; hg19: chr4-102999609;