1-196770707-C-T

Position:

• chr1-196770707-C-T

Variant summary

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

The ENST00000696032.1(ENSG00000289697):​c.3581-8455C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.611 in 133,224 control chromosomes in the GnomAD database, including 31,410 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 0.61 (31410 hom., cov: 23)
• Consequence: ENSG00000289697 ENST00000696032.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.385

Genes affected

ENSG00000289697 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.924 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.196770707C>T		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000289697	ENST00000696032.1	c.3581-8455C>T		intron_variant				ENSP00000512341.1
ENSG00000289697	ENST00000696033.1	c.1160-9090C>T		intron_variant				ENSP00000512342.1

Frequencies

GnomAD3 genomes AF: 0.610 AC: 81232 AN: 133096 Hom.: 31346 Cov.: 23

Gnomad AFR AF: 0.856

Gnomad AMI AF: 0.437

Gnomad AMR AF: 0.694

Gnomad ASJ AF: 0.542

Gnomad EAS AF: 0.946

Gnomad SAS AF: 0.579

Gnomad FIN AF: 0.471

Gnomad MID AF: 0.443

Gnomad NFE AF: 0.474

Gnomad OTH AF: 0.614

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

GnomAD4 genome AF: 0.611 AC: 81357 AN: 133224 Hom.: 31410 Cov.: 23 AF XY: 0.614 AC XY: 39725 AN XY: 64674

Gnomad4 AFR AF: 0.856

Gnomad4 AMR AF: 0.695

Gnomad4 ASJ AF: 0.542

Gnomad4 EAS AF: 0.946

Gnomad4 SAS AF: 0.580

Gnomad4 FIN AF: 0.471

Gnomad4 NFE AF: 0.474

Gnomad4 OTH AF: 0.614

Alfa AF: 0.575 Hom.: 3488

Asia WGS AF: 0.746 AC: 2421 AN: 3246

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.30
DANN	Benign	0.12

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs395998; hg19: chr1-196739837;