rs1471356

Variant names:

• chr14-97836994-A-G
• rs1471356

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 0.27 in 151,900 control chromosomes in the GnomAD database, including 6,044 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 0.27 (6044 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.409
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.361 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: 0.270 AC: 40944 AN: 151782 Hom.: 6032 Cov.: 31

Gnomad AFR AF: 0.366

Gnomad AMI AF: 0.155

Gnomad AMR AF: 0.352

Gnomad ASJ AF: 0.227

Gnomad EAS AF: 0.117

Gnomad SAS AF: 0.178

Gnomad FIN AF: 0.164

Gnomad MID AF: 0.206

Gnomad NFE AF: 0.232

Gnomad OTH AF: 0.248

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

GnomAD4 genome AF: 0.270 AC: 41009 AN: 151900 Hom.: 6044 Cov.: 31 AF XY: 0.267 AC XY: 19812 AN XY: 74230

African (AFR) AF: 0.366 AC: 15153 AN: 41384

American (AMR) AF: 0.352 AC: 5369 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.227 AC: 787 AN: 3466

East Asian (EAS) AF: 0.117 AC: 603 AN: 5144

South Asian (SAS) AF: 0.178 AC: 857 AN: 4820

European-Finnish (FIN) AF: 0.164 AC: 1732 AN: 10566

Middle Eastern (MID) AF: 0.204 AC: 60 AN: 294

European-Non Finnish (NFE) AF: 0.232 AC: 15784 AN: 67952

Other (OTH) AF: 0.247 AC: 523 AN: 2114

Alfa AF: 0.248 Hom.: 16519

Bravo AF: 0.290

Asia WGS AF: 0.166 AC: 576 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.47
DANN	Benign	0.66
PhyloP100		-0.41

Splicing

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

Other links and lift over

dbSNP: rs1471356; hg19: chr14-98303331;