4-102095704-G-T

Variant names:

• chr4-102095704-G-T
• rs12641017

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 0.0364 in 152,274 control chromosomes in the GnomAD database, including 156 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 0.036 (156 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.531

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0744 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: 0.0364 AC: 5537 AN: 152156 Hom.: 154 Cov.: 33

Gnomad AFR AF: 0.0132

Gnomad AMI AF: 0.0789

Gnomad AMR AF: 0.0372

Gnomad ASJ AF: 0.0666

Gnomad EAS AF: 0.0806

Gnomad SAS AF: 0.0551

Gnomad FIN AF: 0.0240

Gnomad MID AF: 0.0285

Gnomad NFE AF: 0.0456

Gnomad OTH AF: 0.0331

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

GnomAD4 genome AF: 0.0364 AC: 5538 AN: 152274 Hom.: 156 Cov.: 33 AF XY: 0.0365 AC XY: 2716 AN XY: 74460

Gnomad4 AFR AF: 0.0132

Gnomad4 AMR AF: 0.0369

Gnomad4 ASJ AF: 0.0666

Gnomad4 EAS AF: 0.0808

Gnomad4 SAS AF: 0.0553

Gnomad4 FIN AF: 0.0240

Gnomad4 NFE AF: 0.0455

Gnomad4 OTH AF: 0.0365

Alfa AF: 0.0353 Hom.: 52

Bravo AF: 0.0363

Asia WGS AF: 0.0860 AC: 298 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	0.026
DANN	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12641017; hg19: chr4-103016861;