rs248471

Variant names:

• chr5-141809602-G-A
• rs248471
• ENST00000750509.1:n.249C>T

Variant summary

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

The ENST00000750509.1(ENSG00000297721):​n.249C>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 0.509 in 151,864 control chromosomes in the GnomAD database, including 20,097 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 0.51 (20097 hom., cov: 31)
• Consequence: ENSG00000297721 ENST00000750509.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0640
• Publications: 11 publications found

Genes affected

ENSG00000297721 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.69).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.661 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107986454	XR_001742906.2	n.9064C>T		non_coding_transcript_exon_variant	Exon 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000297721	ENST00000750509.1	n.249C>T		non_coding_transcript_exon_variant	Exon 3 of 4
ENSG00000297721	ENST00000750510.1	n.*152C>T		downstream_gene_variant
ENSG00000297721	ENST00000750511.1	n.*180C>T		downstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.509 AC: 77209 AN: 151746 Hom.: 20073 Cov.: 31

Gnomad AFR AF: 0.565

Gnomad AMI AF: 0.544

Gnomad AMR AF: 0.530

Gnomad ASJ AF: 0.390

Gnomad EAS AF: 0.678

Gnomad SAS AF: 0.378

Gnomad FIN AF: 0.557

Gnomad MID AF: 0.370

Gnomad NFE AF: 0.466

Gnomad OTH AF: 0.475

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

GnomAD4 genome AF: 0.509 AC: 77263 AN: 151864 Hom.: 20097 Cov.: 31 AF XY: 0.511 AC XY: 37879 AN XY: 74196

African (AFR) AF: 0.565 AC: 23394 AN: 41426

American (AMR) AF: 0.531 AC: 8105 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.390 AC: 1353 AN: 3466

East Asian (EAS) AF: 0.680 AC: 3489 AN: 5134

South Asian (SAS) AF: 0.379 AC: 1819 AN: 4804

European-Finnish (FIN) AF: 0.557 AC: 5871 AN: 10536

Middle Eastern (MID) AF: 0.381 AC: 112 AN: 294

European-Non Finnish (NFE) AF: 0.466 AC: 31632 AN: 67912

Other (OTH) AF: 0.471 AC: 993 AN: 2110

Alfa AF: 0.477 Hom.: 57873

Bravo AF: 0.514

Asia WGS AF: 0.519 AC: 1801 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.69
CADD	Benign	8.1
DANN	Benign	0.83
PhyloP100		0.064

Splicing

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

Other links and lift over

dbSNP: rs248471; hg19: chr5-141189168;