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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000750509.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000297721	ENST00000750509.1		n.249C>T		non_coding_transcript_exon	Exon 3 of 4
	ENSG00000297721	ENST00000750510.1		n.*152C>T		downstream_gene	N/A
	ENSG00000297721	ENST00000750511.1		n.*180C>T		downstream_gene	N/A

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 v4.9

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs248471;

hg19: chr5-141189168;