chr1-159683809-C-T

Variant names:

• chr1-159683809-C-T
• rs1470515
• ENST00000751816.1:n.107+23120C>T

Variant summary

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

The ENST00000751816.1(ENSG00000297913):​n.107+23120C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.36 in 151,966 control chromosomes in the GnomAD database, including 10,377 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 0.36 (10377 hom., cov: 31)
• Consequence: ENSG00000297913 ENST00000751816.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.762
• Publications: 16 publications found

Genes affected

ENSG00000297913 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.563 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000751816.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000297913	ENST00000751816.1		n.107+23120C>T		intron	N/A
	ENSG00000297913	ENST00000751817.1		n.109+23120C>T		intron	N/A
	ENSG00000297913	ENST00000751818.1		n.62+23120C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.360 AC: 54683 AN: 151846 Hom.: 10370 Cov.: 31

Gnomad AFR AF: 0.249

Gnomad AMI AF: 0.573

Gnomad AMR AF: 0.414

Gnomad ASJ AF: 0.380

Gnomad EAS AF: 0.581

Gnomad SAS AF: 0.335

Gnomad FIN AF: 0.391

Gnomad MID AF: 0.360

Gnomad NFE AF: 0.391

Gnomad OTH AF: 0.374

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

GnomAD4 genome AF: 0.360 AC: 54711 AN: 151966 Hom.: 10377 Cov.: 31 AF XY: 0.362 AC XY: 26882 AN XY: 74278

African (AFR) AF: 0.249 AC: 10339 AN: 41446

American (AMR) AF: 0.414 AC: 6332 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.380 AC: 1319 AN: 3470

East Asian (EAS) AF: 0.580 AC: 2974 AN: 5128

South Asian (SAS) AF: 0.335 AC: 1616 AN: 4818

European-Finnish (FIN) AF: 0.391 AC: 4128 AN: 10566

Middle Eastern (MID) AF: 0.361 AC: 106 AN: 294

European-Non Finnish (NFE) AF: 0.391 AC: 26591 AN: 67948

Other (OTH) AF: 0.373 AC: 786 AN: 2110

Alfa AF: 0.383 Hom.: 14981

Bravo AF: 0.357

Asia WGS AF: 0.443 AC: 1542 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	4.0
DANN	Benign	0.62
PhyloP100		0.76

Splicing

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

Other links and lift over

dbSNP: rs1470515; hg19: chr1-159653599;