4-99406180-T-G

Variant names:

• chr4-99406180-T-G
• rs2083687

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.358 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

Gnomad4 AFR AF: 0.276

Gnomad4 AMR AF: 0.320

Gnomad4 ASJ AF: 0.300

Gnomad4 EAS AF: 0.619

Gnomad4 SAS AF: 0.509

Gnomad4 FIN AF: 0.359

Gnomad4 NFE AF: 0.387

Gnomad4 OTH AF: 0.357

Alfa AF: 0.214 Hom.: 502

Bravo AF: 0.343

Asia WGS AF: 0.448 AC: 1556 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2083687; hg19: chr4-100327337;