4-99406180-T-G

Variant names:

• chr4-99406180-T-G
• rs2083687

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 0.358 in 147,932 control chromosomes in the GnomAD database, including 9,715 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 0.36 (9715 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.932
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.601 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.358 AC: 52891 AN: 147850 Hom.: 9711 Cov.: 30

Gnomad AFR AF: 0.276

Gnomad AMI AF: 0.306

Gnomad AMR AF: 0.320

Gnomad ASJ AF: 0.300

Gnomad EAS AF: 0.619

Gnomad SAS AF: 0.509

Gnomad FIN AF: 0.359

Gnomad MID AF: 0.437

Gnomad NFE AF: 0.387

Gnomad OTH AF: 0.356

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

GnomAD4 genome AF: 0.358 AC: 52924 AN: 147932 Hom.: 9715 Cov.: 30 AF XY: 0.361 AC XY: 25961 AN XY: 71974

African (AFR) AF: 0.276 AC: 11048 AN: 40008

American (AMR) AF: 0.320 AC: 4743 AN: 14820

Ashkenazi Jewish (ASJ) AF: 0.300 AC: 1031 AN: 3436

East Asian (EAS) AF: 0.619 AC: 3159 AN: 5106

South Asian (SAS) AF: 0.509 AC: 2407 AN: 4728

European-Finnish (FIN) AF: 0.359 AC: 3316 AN: 9246

Middle Eastern (MID) AF: 0.435 AC: 121 AN: 278

European-Non Finnish (NFE) AF: 0.387 AC: 26086 AN: 67346

Other (OTH) AF: 0.357 AC: 739 AN: 2068

Alfa AF: 0.221 Hom.: 534

Bravo AF: 0.343

Asia WGS AF: 0.448 AC: 1556 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	5.1
DANN	Benign	0.28
PhyloP100		0.93

Splicing

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

Other links and lift over

dbSNP: rs2083687; hg19: chr4-100327337;