rs1205106

chr14-71802951-G-A

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 0.56 in 151,892 control chromosomes in the GnomAD database, including 23,879 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 0.56 (23879 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.819

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.71).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.699 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: 0.560 AC: 85011 AN: 151774 Hom.: 23856 Cov.: 31

Gnomad AFR AF: 0.550

Gnomad AMI AF: 0.775

Gnomad AMR AF: 0.579

Gnomad ASJ AF: 0.679

Gnomad EAS AF: 0.593

Gnomad SAS AF: 0.720

Gnomad FIN AF: 0.512

Gnomad MID AF: 0.634

Gnomad NFE AF: 0.545

Gnomad OTH AF: 0.597

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

GnomAD4 genome AF: 0.560 AC: 85078 AN: 151892 Hom.: 23879 Cov.: 31 AF XY: 0.561 AC XY: 41673 AN XY: 74242

Gnomad4 AFR AF: 0.550

Gnomad4 AMR AF: 0.579

Gnomad4 ASJ AF: 0.679

Gnomad4 EAS AF: 0.594

Gnomad4 SAS AF: 0.719

Gnomad4 FIN AF: 0.512

Gnomad4 NFE AF: 0.545

Gnomad4 OTH AF: 0.600

Alfa AF: 0.562 Hom.: 13660

Bravo AF: 0.562

Asia WGS AF: 0.649 AC: 2255 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.71
Cadd	Benign	12
Dann	Benign	0.84

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1205106; hg19: chr14-72269668;