chr1-198361441-C-T

Variant names:

• chr1-198361441-C-T
• rs1008984
• ENST00000792155.1:n.102+5761C>T

Variant summary

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

The ENST00000792155.1(ENSG00000303141):​n.102+5761C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.297 in 151,802 control chromosomes in the GnomAD database, including 10,754 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 0.30 (10754 hom., cov: 32)
• Consequence: ENSG00000303141 ENST00000792155.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -5.44
• Publications: 2 publications found

Genes affected

ENSG00000303141 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.612 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000303141	ENST00000792155.1	n.102+5761C>T		intron_variant	Intron 1 of 3
ENSG00000303141	ENST00000792156.1	n.78+5761C>T		intron_variant	Intron 1 of 4
ENSG00000303141	ENST00000792157.1	n.79-5114C>T		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.297 AC: 45001 AN: 151684 Hom.: 10712 Cov.: 32

Gnomad AFR AF: 0.619

Gnomad AMI AF: 0.0746

Gnomad AMR AF: 0.367

Gnomad ASJ AF: 0.145

Gnomad EAS AF: 0.455

Gnomad SAS AF: 0.415

Gnomad FIN AF: 0.145

Gnomad MID AF: 0.161

Gnomad NFE AF: 0.101

Gnomad OTH AF: 0.262

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

GnomAD4 genome AF: 0.297 AC: 45111 AN: 151802 Hom.: 10754 Cov.: 32 AF XY: 0.304 AC XY: 22512 AN XY: 74168

African (AFR) AF: 0.619 AC: 25616 AN: 41398

American (AMR) AF: 0.368 AC: 5596 AN: 15204

Ashkenazi Jewish (ASJ) AF: 0.145 AC: 504 AN: 3464

East Asian (EAS) AF: 0.456 AC: 2345 AN: 5148

South Asian (SAS) AF: 0.414 AC: 1994 AN: 4814

European-Finnish (FIN) AF: 0.145 AC: 1529 AN: 10554

Middle Eastern (MID) AF: 0.167 AC: 49 AN: 294

European-Non Finnish (NFE) AF: 0.101 AC: 6850 AN: 67906

Other (OTH) AF: 0.266 AC: 560 AN: 2108

Alfa AF: 0.206 Hom.: 2219

Bravo AF: 0.327

Asia WGS AF: 0.454 AC: 1579 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.034
DANN	Benign	0.16
PhyloP100		-5.4

Splicing

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

Other links and lift over

dbSNP: rs1008984; hg19: chr1-198330571;