chr1-29761184-G-T

Variant names:

• chr1-29761184-G-T
• rs10914351
• ENST00000641702.1:n.376+792G>T

Variant summary

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

The ENST00000641702.1(ENSG00000284676):​n.376+792G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0556 in 152,204 control chromosomes in the GnomAD database, including 470 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 0.056 (470 hom., cov: 32)
• Consequence: ENSG00000284676 ENST00000641702.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0210
• Publications: 2 publications found

Genes affected

ENSG00000284676 (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 = 0.223 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000641702.1. 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000284676	ENST00000641702.1		n.376+792G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0556 AC: 8454 AN: 152084 Hom.: 468 Cov.: 32

Gnomad AFR AF: 0.0841

Gnomad AMI AF: 0.0515

Gnomad AMR AF: 0.0327

Gnomad ASJ AF: 0.0746

Gnomad EAS AF: 0.234

Gnomad SAS AF: 0.216

Gnomad FIN AF: 0.0266

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.0223

Gnomad OTH AF: 0.0488

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

GnomAD4 genome AF: 0.0556 AC: 8462 AN: 152204 Hom.: 470 Cov.: 32 AF XY: 0.0600 AC XY: 4466 AN XY: 74420

African (AFR) AF: 0.0841 AC: 3490 AN: 41502

American (AMR) AF: 0.0326 AC: 499 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.0746 AC: 259 AN: 3472

East Asian (EAS) AF: 0.234 AC: 1208 AN: 5170

South Asian (SAS) AF: 0.216 AC: 1038 AN: 4804

European-Finnish (FIN) AF: 0.0266 AC: 283 AN: 10620

Middle Eastern (MID) AF: 0.0442 AC: 13 AN: 294

European-Non Finnish (NFE) AF: 0.0223 AC: 1517 AN: 68028

Other (OTH) AF: 0.0511 AC: 108 AN: 2114

Alfa AF: 0.0413 Hom.: 198

Bravo AF: 0.0552

Asia WGS AF: 0.204 AC: 709 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.2
DANN	Benign	0.63
PhyloP100		-0.021

Splicing

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

Other links and lift over

dbSNP: rs10914351; hg19: chr1-30234031;