rs7148997

chr14-21542046-G-C

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 0.377 in 152,104 control chromosomes in the GnomAD database, including 11,687 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 0.38 (11687 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.98

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.468 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: 0.377 AC: 57293 AN: 151986 Hom.: 11681 Cov.: 32

Gnomad AFR AF: 0.318

Gnomad AMI AF: 0.270

Gnomad AMR AF: 0.477

Gnomad ASJ AF: 0.486

Gnomad EAS AF: 0.0473

Gnomad SAS AF: 0.298

Gnomad FIN AF: 0.239

Gnomad MID AF: 0.449

Gnomad NFE AF: 0.438

Gnomad OTH AF: 0.379

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

GnomAD4 genome AF: 0.377 AC: 57329 AN: 152104 Hom.: 11687 Cov.: 32 AF XY: 0.368 AC XY: 27349 AN XY: 74360

Gnomad4 AFR AF: 0.318

Gnomad4 AMR AF: 0.477

Gnomad4 ASJ AF: 0.486

Gnomad4 EAS AF: 0.0472

Gnomad4 SAS AF: 0.298

Gnomad4 FIN AF: 0.239

Gnomad4 NFE AF: 0.438

Gnomad4 OTH AF: 0.375

Alfa AF: 0.402 Hom.: 1558

Bravo AF: 0.389

Asia WGS AF: 0.205 AC: 717 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	0.13
Dann	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7148997; hg19: chr14-22010192;