rs318497

Variant names:

• chr6-2912043-G-A
• rs318497
• ENST00000454998.1:n.71C>T

Your query was ambiguous. Multiple possible variants found:

• chr6-2912043-G-A
• chr6-2912043-G-C
• chr6-2912043-G-T

Variant summary

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

The ENST00000454998.1(ENSG00000232999):​n.71C>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 0.456 in 151,886 control chromosomes in the GnomAD database, including 15,977 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 0.46 (15976 hom., cov: 30)
  • Exomes 𝑓: 0.28 (1 hom.)
• Consequence: ENSG00000232999 ENST00000454998.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.246
• Publications: 17 publications found

Genes affected

ENSG00000232999 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.538 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
ENSG00000232999	ENST00000454998.1	n.71C>T		non_coding_transcript_exon_variant	Exon 1 of 2	6

Frequencies

GnomAD3 genomes AF: 0.456 AC: 69177 AN: 151708 Hom.: 15982 Cov.: 30

Gnomad AFR AF: 0.425

Gnomad AMI AF: 0.447

Gnomad AMR AF: 0.488

Gnomad ASJ AF: 0.564

Gnomad EAS AF: 0.556

Gnomad SAS AF: 0.350

Gnomad FIN AF: 0.362

Gnomad MID AF: 0.449

Gnomad NFE AF: 0.476

Gnomad OTH AF: 0.490

GnomAD4 exome AF: 0.283 AC: 17 AN: 60 Hom.: 1 Cov.: 0 AF XY: 0.235 AC XY: 8 AN XY: 34

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.273 AC: 6 AN: 22

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.286 AC: 8 AN: 28

Other (OTH) AF: 0.300 AC: 3 AN: 10

GnomAD4 genome AF: 0.456 AC: 69187 AN: 151826 Hom.: 15976 Cov.: 30 AF XY: 0.448 AC XY: 33260 AN XY: 74174

African (AFR) AF: 0.424 AC: 17537 AN: 41370

American (AMR) AF: 0.488 AC: 7440 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.564 AC: 1954 AN: 3466

East Asian (EAS) AF: 0.555 AC: 2855 AN: 5142

South Asian (SAS) AF: 0.350 AC: 1683 AN: 4808

European-Finnish (FIN) AF: 0.362 AC: 3809 AN: 10534

Middle Eastern (MID) AF: 0.449 AC: 132 AN: 294

European-Non Finnish (NFE) AF: 0.476 AC: 32344 AN: 67942

Other (OTH) AF: 0.487 AC: 1027 AN: 2110

Alfa AF: 0.475 Hom.: 55577

Bravo AF: 0.471

Asia WGS AF: 0.461 AC: 1601 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	4.8
DANN	Benign	0.66
PhyloP100		-0.25

Splicing

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

Other links and lift over

dbSNP: rs318497; hg19: chr6-2912277;