ENST00000612269.3:n.983C>T

Variant names:

• chr19-34733565-G-A
• rs7624
• ENST00000612269.3:n.983C>T

Variant summary

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

The ENST00000612269.3(ENSG00000274104):​n.983C>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 0.281 in 151,900 control chromosomes in the GnomAD database, including 6,547 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 0.28 (6547 hom., cov: 31)
  • Exomes 𝑓: 0.15 (0 hom.)
• Consequence: ENSG00000274104 ENST00000612269.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.793
• Publications: 11 publications found

Genes affected

ENSG00000274104 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.333 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
ENSG00000274104	ENST00000612269.3	n.983C>T		non_coding_transcript_exon_variant	Exon 1 of 1	6

Frequencies

GnomAD3 genomes AF: 0.282 AC: 42724 AN: 151762 Hom.: 6555 Cov.: 31

Gnomad AFR AF: 0.174

Gnomad AMI AF: 0.568

Gnomad AMR AF: 0.277

Gnomad ASJ AF: 0.278

Gnomad EAS AF: 0.277

Gnomad SAS AF: 0.233

Gnomad FIN AF: 0.352

Gnomad MID AF: 0.363

Gnomad NFE AF: 0.337

Gnomad OTH AF: 0.290

GnomAD4 exome AF: 0.150 AC: 3 AN: 20 Hom.: 0 Cov.: 0 AF XY: 0.200 AC XY: 2 AN XY: 10

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: 0.00 AC: 0 AN: 4

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.167 AC: 2 AN: 12

Other (OTH) AF: 0.250 AC: 1 AN: 4

GnomAD4 genome AF: 0.281 AC: 42721 AN: 151880 Hom.: 6547 Cov.: 31 AF XY: 0.282 AC XY: 20946 AN XY: 74228

African (AFR) AF: 0.174 AC: 7190 AN: 41418

American (AMR) AF: 0.276 AC: 4219 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.278 AC: 965 AN: 3466

East Asian (EAS) AF: 0.277 AC: 1417 AN: 5114

South Asian (SAS) AF: 0.233 AC: 1119 AN: 4808

European-Finnish (FIN) AF: 0.352 AC: 3719 AN: 10554

Middle Eastern (MID) AF: 0.353 AC: 103 AN: 292

European-Non Finnish (NFE) AF: 0.336 AC: 22861 AN: 67938

Other (OTH) AF: 0.290 AC: 612 AN: 2112

Alfa AF: 0.319 Hom.: 16982

Bravo AF: 0.272

Asia WGS AF: 0.254 AC: 882 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.96
DANN	Benign	0.80
PhyloP100		-0.79

Splicing

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

Other links and lift over

dbSNP: rs7624; hg19: chr19-35224470;