rs1885094

Variant names:

• chr14-60732627-C-T
• rs1885094

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 0.671 in 152,020 control chromosomes in the GnomAD database, including 34,693 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 0.67 (34693 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.62
• Publications: 6 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.719 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: 0.672 AC: 102031 AN: 151902 Hom.: 34696 Cov.: 31

Gnomad AFR AF: 0.576

Gnomad AMI AF: 0.748

Gnomad AMR AF: 0.730

Gnomad ASJ AF: 0.607

Gnomad EAS AF: 0.634

Gnomad SAS AF: 0.647

Gnomad FIN AF: 0.725

Gnomad MID AF: 0.646

Gnomad NFE AF: 0.715

Gnomad OTH AF: 0.685

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

GnomAD4 genome AF: 0.671 AC: 102068 AN: 152020 Hom.: 34693 Cov.: 31 AF XY: 0.672 AC XY: 49957 AN XY: 74316

African (AFR) AF: 0.575 AC: 23825 AN: 41434

American (AMR) AF: 0.730 AC: 11154 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.607 AC: 2105 AN: 3466

East Asian (EAS) AF: 0.633 AC: 3271 AN: 5168

South Asian (SAS) AF: 0.646 AC: 3117 AN: 4822

European-Finnish (FIN) AF: 0.725 AC: 7659 AN: 10558

Middle Eastern (MID) AF: 0.636 AC: 187 AN: 294

European-Non Finnish (NFE) AF: 0.715 AC: 48624 AN: 67986

Other (OTH) AF: 0.684 AC: 1444 AN: 2110

Alfa AF: 0.691 Hom.: 72018

Bravo AF: 0.670

Asia WGS AF: 0.670 AC: 2330 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.019
DANN	Benign	0.37
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs1885094; hg19: chr14-61199345;