rs7148720

Positions:

• chr14-61676071-T-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 0.0349 in 152,242 control chromosomes in the GnomAD database, including 212 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 0.035 (212 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.308

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.153 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0349 AC: 5316 AN: 152124 Hom.: 215 Cov.: 32

Gnomad AFR AF: 0.0502

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0234

Gnomad ASJ AF: 0.0876

Gnomad EAS AF: 0.148

Gnomad SAS AF: 0.162

Gnomad FIN AF: 0.00584

Gnomad MID AF: 0.0759

Gnomad NFE AF: 0.0128

Gnomad OTH AF: 0.0339

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

GnomAD4 genome AF: 0.0349 AC: 5312 AN: 152242 Hom.: 212 Cov.: 32 AF XY: 0.0380 AC XY: 2830 AN XY: 74450

Gnomad4 AFR AF: 0.0500

Gnomad4 AMR AF: 0.0233

Gnomad4 ASJ AF: 0.0876

Gnomad4 EAS AF: 0.147

Gnomad4 SAS AF: 0.162

Gnomad4 FIN AF: 0.00584

Gnomad4 NFE AF: 0.0128

Gnomad4 OTH AF: 0.0331

Alfa AF: 0.0204 Hom.: 22

Bravo AF: 0.0346

Asia WGS AF: 0.126 AC: 438 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	3.9
DANN	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7148720; hg19: chr14-62142789;