chr5-23371531-C-T

Variant names:

• chr5-23371531-C-T
• rs10050856
• ENST00000744988.1:n.620C>T

Variant summary

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

The ENST00000744988.1(ENSG00000297049):​n.620C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.423 in 151,818 control chromosomes in the GnomAD database, including 17,429 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 0.42 (17429 hom., cov: 31)
• Consequence: ENSG00000297049 ENST00000744988.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.455
• Publications: 1 publications found

Genes affected

ENSG00000297049 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.769 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
ENSG00000297049	ENST00000744988.1	n.620C>T		non_coding_transcript_exon_variant	Exon 2 of 2

Frequencies

GnomAD3 genomes AF: 0.423 AC: 64157 AN: 151700 Hom.: 17371 Cov.: 31

Gnomad AFR AF: 0.775

Gnomad AMI AF: 0.247

Gnomad AMR AF: 0.287

Gnomad ASJ AF: 0.358

Gnomad EAS AF: 0.253

Gnomad SAS AF: 0.487

Gnomad FIN AF: 0.216

Gnomad MID AF: 0.269

Gnomad NFE AF: 0.287

Gnomad OTH AF: 0.398

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

GnomAD4 genome AF: 0.423 AC: 64266 AN: 151818 Hom.: 17429 Cov.: 31 AF XY: 0.416 AC XY: 30864 AN XY: 74174

African (AFR) AF: 0.776 AC: 32121 AN: 41406

American (AMR) AF: 0.286 AC: 4369 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.358 AC: 1243 AN: 3468

East Asian (EAS) AF: 0.253 AC: 1306 AN: 5158

South Asian (SAS) AF: 0.485 AC: 2334 AN: 4810

European-Finnish (FIN) AF: 0.216 AC: 2272 AN: 10510

Middle Eastern (MID) AF: 0.259 AC: 75 AN: 290

European-Non Finnish (NFE) AF: 0.287 AC: 19488 AN: 67916

Other (OTH) AF: 0.397 AC: 833 AN: 2100

Alfa AF: 0.255 Hom.: 7226

Bravo AF: 0.439

Asia WGS AF: 0.411 AC: 1423 AN: 3456

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.3
DANN	Benign	0.57
PhyloP100		-0.46

Splicing

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

Other links and lift over

dbSNP: rs10050856; hg19: chr5-23371640;