rs234511

chr15-97004895-T-Achr15-97004895-T-G

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 0.078 in 152,190 control chromosomes in the GnomAD database, including 1,084 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 0.078 (1084 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.113

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.216 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: 0.0777 AC: 11822 AN: 152070 Hom.: 1073 Cov.: 32

Gnomad AFR AF: 0.219

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0621

Gnomad ASJ AF: 0.00432

Gnomad EAS AF: 0.0550

Gnomad SAS AF: 0.0325

Gnomad FIN AF: 0.00254

Gnomad MID AF: 0.0190

Gnomad NFE AF: 0.0173

Gnomad OTH AF: 0.0688

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

GnomAD4 genome AF: 0.0780 AC: 11870 AN: 152190 Hom.: 1084 Cov.: 32 AF XY: 0.0754 AC XY: 5611 AN XY: 74406

Gnomad4 AFR AF: 0.220

Gnomad4 AMR AF: 0.0621

Gnomad4 ASJ AF: 0.00432

Gnomad4 EAS AF: 0.0544

Gnomad4 SAS AF: 0.0332

Gnomad4 FIN AF: 0.00254

Gnomad4 NFE AF: 0.0173

Gnomad4 OTH AF: 0.0685

Alfa AF: 0.00323 Hom.: 1

Bravo AF: 0.0897

Asia WGS AF: 0.0580 AC: 203 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
Cadd	Benign	1.7
Dann	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs234511; hg19: chr15-97548125;