chr1-29761184-G-T

Position:

• chr1-29761184-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000641702.1(ENSG00000284676):​n.376+792G>T variant causes a intron, non coding transcript 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: ENST00000641702.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0210

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000641702.1	n.376+792G>T		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.0841

Gnomad4 AMR AF: 0.0326

Gnomad4 ASJ AF: 0.0746

Gnomad4 EAS AF: 0.234

Gnomad4 SAS AF: 0.216

Gnomad4 FIN AF: 0.0266

Gnomad4 NFE AF: 0.0223

Gnomad4 OTH AF: 0.0511

Alfa AF: 0.0417 Hom.: 188

Bravo AF: 0.0552

Asia WGS AF: 0.204 AC: 709 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10914351; hg19: chr1-30234031;