rs236768

chr4-102154826-G-Achr4-102154826-G-T

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 0.793 in 152,180 control chromosomes in the GnomAD database, including 48,052 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 0.79 (48052 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.831

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.813 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.793 AC: 120524 AN: 152062 Hom.: 48018 Cov.: 32

Gnomad AFR AF: 0.781

Gnomad AMI AF: 0.825

Gnomad AMR AF: 0.721

Gnomad ASJ AF: 0.731

Gnomad EAS AF: 0.674

Gnomad SAS AF: 0.826

Gnomad FIN AF: 0.842

Gnomad MID AF: 0.785

Gnomad NFE AF: 0.818

Gnomad OTH AF: 0.770

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

GnomAD4 genome AF: 0.793 AC: 120615 AN: 152180 Hom.: 48052 Cov.: 32 AF XY: 0.790 AC XY: 58809 AN XY: 74404

Gnomad4 AFR AF: 0.781

Gnomad4 AMR AF: 0.722

Gnomad4 ASJ AF: 0.731

Gnomad4 EAS AF: 0.673

Gnomad4 SAS AF: 0.825

Gnomad4 FIN AF: 0.842

Gnomad4 NFE AF: 0.818

Gnomad4 OTH AF: 0.767

Alfa AF: 0.813 Hom.: 25174

Bravo AF: 0.781

Asia WGS AF: 0.739 AC: 2570 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.18
Dann	Benign	0.20

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs236768; hg19: chr4-103075983;