rs11627513

chr14-97072834-C-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 0.143 in 152,090 control chromosomes in the GnomAD database, including 2,019 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 0.14 (2019 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.246

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.199 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: 0.143 AC: 21727 AN: 151970 Hom.: 2021 Cov.: 32

Gnomad AFR AF: 0.0412

Gnomad AMI AF: 0.112

Gnomad AMR AF: 0.170

Gnomad ASJ AF: 0.233

Gnomad EAS AF: 0.00135

Gnomad SAS AF: 0.0753

Gnomad FIN AF: 0.194

Gnomad MID AF: 0.197

Gnomad NFE AF: 0.202

Gnomad OTH AF: 0.150

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

GnomAD4 genome AF: 0.143 AC: 21724 AN: 152090 Hom.: 2019 Cov.: 32 AF XY: 0.141 AC XY: 10482 AN XY: 74348

Gnomad4 AFR AF: 0.0410

Gnomad4 AMR AF: 0.170

Gnomad4 ASJ AF: 0.233

Gnomad4 EAS AF: 0.00135

Gnomad4 SAS AF: 0.0760

Gnomad4 FIN AF: 0.194

Gnomad4 NFE AF: 0.202

Gnomad4 OTH AF: 0.148

Alfa AF: 0.168 Hom.: 412

Bravo AF: 0.138

Asia WGS AF: 0.0360 AC: 125 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	7.9
Dann	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11627513; hg19: chr14-97539171;