rs7146371

chr14-71173972-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 0.62 in 152,028 control chromosomes in the GnomAD database, including 29,707 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 0.62 (29707 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.90

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.729 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: 0.620 AC: 94216 AN: 151912 Hom.: 29676 Cov.: 32

Gnomad AFR AF: 0.735

Gnomad AMI AF: 0.739

Gnomad AMR AF: 0.569

Gnomad ASJ AF: 0.651

Gnomad EAS AF: 0.369

Gnomad SAS AF: 0.607

Gnomad FIN AF: 0.538

Gnomad MID AF: 0.750

Gnomad NFE AF: 0.591

Gnomad OTH AF: 0.616

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

GnomAD4 genome AF: 0.620 AC: 94295 AN: 152028 Hom.: 29707 Cov.: 32 AF XY: 0.615 AC XY: 45705 AN XY: 74290

Gnomad4 AFR AF: 0.736

Gnomad4 AMR AF: 0.569

Gnomad4 ASJ AF: 0.651

Gnomad4 EAS AF: 0.369

Gnomad4 SAS AF: 0.607

Gnomad4 FIN AF: 0.538

Gnomad4 NFE AF: 0.591

Gnomad4 OTH AF: 0.611

Alfa AF: 0.600 Hom.: 57471

Bravo AF: 0.627

Asia WGS AF: 0.489 AC: 1706 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
Cadd	Benign	0.17
Dann	Benign	0.29

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7146371; hg19: chr14-71640689;