rs923485

Variant names:

• chr14-62466359-T-C
• rs923485
• ENST00000743723.1:n.587-37685T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000743723.1(ENSG00000296937):​n.587-37685T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.22 in 151,852 control chromosomes in the GnomAD database, including 3,943 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 0.22 (3943 hom., cov: 32)
• Consequence: ENSG00000296937 ENST00000743723.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.28
• Publications: 3 publications found

Genes affected

ENSG00000296937 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.29 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105370529	XR_943932.3	n.126-37682T>C		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000296937	ENST00000743723.1	n.587-37685T>C		intron_variant	Intron 2 of 4
ENSG00000296937	ENST00000743724.1	n.588-37685T>C		intron_variant	Intron 2 of 3
ENSG00000296937	ENST00000743725.1	n.333-37682T>C		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.220 AC: 33310 AN: 151734 Hom.: 3931 Cov.: 32

Gnomad AFR AF: 0.271

Gnomad AMI AF: 0.103

Gnomad AMR AF: 0.297

Gnomad ASJ AF: 0.250

Gnomad EAS AF: 0.154

Gnomad SAS AF: 0.157

Gnomad FIN AF: 0.199

Gnomad MID AF: 0.269

Gnomad NFE AF: 0.183

Gnomad OTH AF: 0.230

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

GnomAD4 genome AF: 0.220 AC: 33373 AN: 151852 Hom.: 3943 Cov.: 32 AF XY: 0.221 AC XY: 16376 AN XY: 74234

African (AFR) AF: 0.271 AC: 11249 AN: 41460

American (AMR) AF: 0.297 AC: 4513 AN: 15208

Ashkenazi Jewish (ASJ) AF: 0.250 AC: 868 AN: 3466

East Asian (EAS) AF: 0.153 AC: 791 AN: 5160

South Asian (SAS) AF: 0.159 AC: 767 AN: 4824

European-Finnish (FIN) AF: 0.199 AC: 2112 AN: 10594

Middle Eastern (MID) AF: 0.269 AC: 79 AN: 294

European-Non Finnish (NFE) AF: 0.183 AC: 12405 AN: 67824

Other (OTH) AF: 0.235 AC: 495 AN: 2110

Alfa AF: 0.209 Hom.: 1052

Bravo AF: 0.233

Asia WGS AF: 0.184 AC: 639 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	2.8
DANN	Benign	0.58
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs923485; hg19: chr14-62933077;