chr1-181847374-T-C

Variant names:

• chr1-181847374-T-C
• rs695072
• ENST00000717053.1:n.288-11738A>G

Variant summary

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

The ENST00000717053.1(ENSG00000287452):​n.288-11738A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.337 in 152,024 control chromosomes in the GnomAD database, including 8,870 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 0.34 (8870 hom., cov: 31)
• Consequence: ENSG00000287452 ENST00000717053.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.600
• Publications: 3 publications found

Genes affected

ENSG00000287452 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.367 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
ENSG00000287452	ENST00000717053.1	n.288-11738A>G		intron_variant	Intron 1 of 3
ENSG00000287452	ENST00000717054.1	n.293-11738A>G		intron_variant	Intron 1 of 3
ENSG00000287452	ENST00000717055.1	n.81-11738A>G		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.337 AC: 51134 AN: 151906 Hom.: 8861 Cov.: 31

Gnomad AFR AF: 0.305

Gnomad AMI AF: 0.343

Gnomad AMR AF: 0.326

Gnomad ASJ AF: 0.282

Gnomad EAS AF: 0.0882

Gnomad SAS AF: 0.355

Gnomad FIN AF: 0.374

Gnomad MID AF: 0.494

Gnomad NFE AF: 0.371

Gnomad OTH AF: 0.370

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

GnomAD4 genome AF: 0.337 AC: 51163 AN: 152024 Hom.: 8870 Cov.: 31 AF XY: 0.333 AC XY: 24759 AN XY: 74300

African (AFR) AF: 0.305 AC: 12638 AN: 41468

American (AMR) AF: 0.326 AC: 4985 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.282 AC: 979 AN: 3468

East Asian (EAS) AF: 0.0876 AC: 454 AN: 5180

South Asian (SAS) AF: 0.355 AC: 1710 AN: 4822

European-Finnish (FIN) AF: 0.374 AC: 3940 AN: 10542

Middle Eastern (MID) AF: 0.497 AC: 146 AN: 294

European-Non Finnish (NFE) AF: 0.371 AC: 25222 AN: 67958

Other (OTH) AF: 0.368 AC: 777 AN: 2110

Alfa AF: 0.356 Hom.: 41849

Bravo AF: 0.329

Asia WGS AF: 0.225 AC: 782 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	3.3
DANN	Benign	0.74
PhyloP100		0.60

Splicing

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

Other links and lift over

dbSNP: rs695072; hg19: chr1-181816509;