rs1156446

Variant names:

• chr14-70038846-G-A
• rs1156446

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 0.165 in 152,220 control chromosomes in the GnomAD database, including 2,815 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 0.16 (2815 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.113
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.389 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: 0.165 AC: 25084 AN: 152100 Hom.: 2805 Cov.: 32

Gnomad AFR AF: 0.0466

Gnomad AMI AF: 0.132

Gnomad AMR AF: 0.288

Gnomad ASJ AF: 0.136

Gnomad EAS AF: 0.403

Gnomad SAS AF: 0.193

Gnomad FIN AF: 0.216

Gnomad MID AF: 0.133

Gnomad NFE AF: 0.183

Gnomad OTH AF: 0.181

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

GnomAD4 genome AF: 0.165 AC: 25099 AN: 152220 Hom.: 2815 Cov.: 32 AF XY: 0.171 AC XY: 12754 AN XY: 74408

African (AFR) AF: 0.0465 AC: 1932 AN: 41548

American (AMR) AF: 0.289 AC: 4424 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.136 AC: 471 AN: 3470

East Asian (EAS) AF: 0.404 AC: 2089 AN: 5176

South Asian (SAS) AF: 0.193 AC: 932 AN: 4830

European-Finnish (FIN) AF: 0.216 AC: 2287 AN: 10578

Middle Eastern (MID) AF: 0.129 AC: 38 AN: 294

European-Non Finnish (NFE) AF: 0.183 AC: 12427 AN: 68006

Other (OTH) AF: 0.179 AC: 379 AN: 2112

Alfa AF: 0.185 Hom.: 1093

Bravo AF: 0.167

Asia WGS AF: 0.260 AC: 902 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	9.0
DANN	Benign	0.74
PhyloP100		0.11

Splicing

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

Other links and lift over

dbSNP: rs1156446; hg19: chr14-70505563;