1-196770707-C-T

Variant names:

• chr1-196770707-C-T
• rs395998
• ENST00000696032.1:c.3581-8455C>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 5 publications found

Genes affected

ENSG00000289697 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000696032.1. 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
	ENSG00000289697	ENST00000696032.1		c.3581-8455C>T		intron	N/A	ENSP00000512341.1	A0A8Q3SIA1
	ENSG00000289697	ENST00000696033.1		c.1160-9090C>T		intron	N/A	ENSP00000512342.1	A0A8Q3SID3

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

African (AFR) AF: 0.856 AC: 26834 AN: 31342

American (AMR) AF: 0.695 AC: 9513 AN: 13694

Ashkenazi Jewish (ASJ) AF: 0.542 AC: 1705 AN: 3148

East Asian (EAS) AF: 0.946 AC: 4794 AN: 5068

South Asian (SAS) AF: 0.580 AC: 2179 AN: 3756

European-Finnish (FIN) AF: 0.471 AC: 4603 AN: 9768

Middle Eastern (MID) AF: 0.440 AC: 103 AN: 234

European-Non Finnish (NFE) AF: 0.474 AC: 30143 AN: 63550

Other (OTH) AF: 0.614 AC: 1108 AN: 1806

Alfa AF: 0.575 Hom.: 3488

Asia WGS AF: 0.746 AC: 2421 AN: 3246

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.30
DANN	Benign	0.12
PhyloP100		-0.39

Splicing

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

Other links and lift over

dbSNP: rs395998; hg19: chr1-196739837;