rs2974097

Variant names:

• chr5-86038135-T-A
• rs2974097
• ENST00000767533.1:n.134+29389T>A

Your query was ambiguous. Multiple possible variants found:

• chr5-86038135-T-A
• chr5-86038135-T-C
• chr5-86038135-T-G

Variant summary

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

The ENST00000767533.1(ENSG00000299923):​n.134+29389T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.504 in 151,966 control chromosomes in the GnomAD database, including 20,495 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 0.50 (20495 hom., cov: 32)
• Consequence: ENSG00000299923 ENST00000767533.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.15
• Publications: 1 publications found

Genes affected

ENSG00000299923 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.664 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
ENSG00000299923	ENST00000767533.1	n.134+29389T>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.504 AC: 76522 AN: 151848 Hom.: 20466 Cov.: 32

Gnomad AFR AF: 0.671

Gnomad AMI AF: 0.498

Gnomad AMR AF: 0.561

Gnomad ASJ AF: 0.518

Gnomad EAS AF: 0.165

Gnomad SAS AF: 0.376

Gnomad FIN AF: 0.474

Gnomad MID AF: 0.528

Gnomad NFE AF: 0.428

Gnomad OTH AF: 0.501

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

GnomAD4 genome AF: 0.504 AC: 76594 AN: 151966 Hom.: 20495 Cov.: 32 AF XY: 0.504 AC XY: 37428 AN XY: 74268

African (AFR) AF: 0.671 AC: 27809 AN: 41448

American (AMR) AF: 0.562 AC: 8572 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.518 AC: 1798 AN: 3468

East Asian (EAS) AF: 0.165 AC: 851 AN: 5166

South Asian (SAS) AF: 0.376 AC: 1809 AN: 4816

European-Finnish (FIN) AF: 0.474 AC: 4982 AN: 10520

Middle Eastern (MID) AF: 0.524 AC: 154 AN: 294

European-Non Finnish (NFE) AF: 0.428 AC: 29122 AN: 67972

Other (OTH) AF: 0.494 AC: 1046 AN: 2116

Alfa AF: 0.312 Hom.: 704

Bravo AF: 0.520

Asia WGS AF: 0.291 AC: 1010 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.5
DANN	Benign	0.35
PhyloP100		1.1

Splicing

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

Other links and lift over

dbSNP: rs2974097; hg19: chr5-85333953;