rs7148997

Variant names:

• chr14-21542046-G-C
• rs7148997

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.318 AC: 13186 AN: 41486

American (AMR) AF: 0.477 AC: 7283 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.486 AC: 1685 AN: 3468

East Asian (EAS) AF: 0.0472 AC: 245 AN: 5188

South Asian (SAS) AF: 0.298 AC: 1441 AN: 4828

European-Finnish (FIN) AF: 0.239 AC: 2531 AN: 10570

Middle Eastern (MID) AF: 0.442 AC: 129 AN: 292

European-Non Finnish (NFE) AF: 0.438 AC: 29791 AN: 67978

Other (OTH) AF: 0.375 AC: 792 AN: 2110

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
PhyloP100		-2.0

Splicing

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

Other links and lift over

dbSNP: rs7148997; hg19: chr14-22010192;