1-19983072-A-T

Variant names:

• chr1-19983072-A-T
• rs10916685
• ENST00000747726.1:n.*64T>A

Variant summary

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

The ENST00000747726.1(ENSG00000297402):​n.*64T>A variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.333 in 152,034 control chromosomes in the GnomAD database, including 8,678 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 0.33 (8678 hom., cov: 32)
• Consequence: ENSG00000297402 ENST00000747726.1 downstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.303
• Publications: 4 publications found

Genes affected

ENSG00000297402 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.368 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
ENSG00000297402	ENST00000747726.1	n.*64T>A		downstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.333 AC: 50633 AN: 151916 Hom.: 8675 Cov.: 32

Gnomad AFR AF: 0.290

Gnomad AMI AF: 0.442

Gnomad AMR AF: 0.376

Gnomad ASJ AF: 0.305

Gnomad EAS AF: 0.274

Gnomad SAS AF: 0.320

Gnomad FIN AF: 0.333

Gnomad MID AF: 0.252

Gnomad NFE AF: 0.356

Gnomad OTH AF: 0.320

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

GnomAD4 genome AF: 0.333 AC: 50656 AN: 152034 Hom.: 8678 Cov.: 32 AF XY: 0.333 AC XY: 24760 AN XY: 74312

African (AFR) AF: 0.290 AC: 12008 AN: 41458

American (AMR) AF: 0.376 AC: 5751 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.305 AC: 1060 AN: 3470

East Asian (EAS) AF: 0.275 AC: 1425 AN: 5180

South Asian (SAS) AF: 0.320 AC: 1544 AN: 4826

European-Finnish (FIN) AF: 0.333 AC: 3510 AN: 10536

Middle Eastern (MID) AF: 0.260 AC: 76 AN: 292

European-Non Finnish (NFE) AF: 0.356 AC: 24210 AN: 67968

Other (OTH) AF: 0.317 AC: 669 AN: 2110

Alfa AF: 0.335 Hom.: 1089

Bravo AF: 0.338

Asia WGS AF: 0.319 AC: 1109 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	9.1
DANN	Benign	0.92
PhyloP100		0.30

Splicing

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

Other links and lift over

dbSNP: rs10916685; hg19: chr1-20309565; COSMIC: COSV64287665;