chr1-159707006-G-A

Variant names:

• chr1-159707006-G-A
• rs2808629
• ENST00000751816.1:n.108-19521G>A

Variant summary

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

The ENST00000751816.1(ENSG00000297913):​n.108-19521G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.312 in 151,864 control chromosomes in the GnomAD database, including 7,980 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 0.31 (7980 hom., cov: 32)
• Consequence: ENSG00000297913 ENST00000751816.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.343
• Publications: 22 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=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.565 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

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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000297913	ENST00000751816.1		n.108-19521G>A		intron	N/A
	ENSG00000297913	ENST00000751817.1		n.110-19521G>A		intron	N/A
	ENSG00000297913	ENST00000751818.1		n.63-19521G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.312 AC: 47353 AN: 151746 Hom.: 7973 Cov.: 32

Gnomad AFR AF: 0.198

Gnomad AMI AF: 0.223

Gnomad AMR AF: 0.372

Gnomad ASJ AF: 0.359

Gnomad EAS AF: 0.583

Gnomad SAS AF: 0.314

Gnomad FIN AF: 0.376

Gnomad MID AF: 0.339

Gnomad NFE AF: 0.335

Gnomad OTH AF: 0.330

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

GnomAD4 genome AF: 0.312 AC: 47379 AN: 151864 Hom.: 7980 Cov.: 32 AF XY: 0.317 AC XY: 23515 AN XY: 74212

African (AFR) AF: 0.198 AC: 8219 AN: 41448

American (AMR) AF: 0.373 AC: 5685 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.359 AC: 1244 AN: 3468

East Asian (EAS) AF: 0.583 AC: 3012 AN: 5168

South Asian (SAS) AF: 0.314 AC: 1507 AN: 4794

European-Finnish (FIN) AF: 0.376 AC: 3958 AN: 10526

Middle Eastern (MID) AF: 0.333 AC: 98 AN: 294

European-Non Finnish (NFE) AF: 0.335 AC: 22757 AN: 67886

Other (OTH) AF: 0.330 AC: 696 AN: 2110

Alfa AF: 0.290 Hom.: 2606

Bravo AF: 0.306

Asia WGS AF: 0.440 AC: 1527 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.6
DANN	Benign	0.51
PhyloP100		0.34

Splicing

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

Other links and lift over

dbSNP: rs2808629; hg19: chr1-159676796;