chr1-243852691-C-T

Variant names:

• chr1-243852691-C-T
• rs4430311
• ENST00000808497.1:n.112+2966C>T

Variant summary

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

The ENST00000808497.1(ENSG00000305096):​n.112+2966C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.587 in 151,894 control chromosomes in the GnomAD database, including 27,295 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 0.59 (27295 hom., cov: 31)
• Consequence: ENSG00000305096 ENST00000808497.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0460
• Publications: 16 publications found

Genes affected

ENSG00000305096 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.666 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
ENSG00000305096	ENST00000808497.1	n.112+2966C>T		intron_variant	Intron 1 of 3
ENSG00000305096	ENST00000808498.1	n.51+2966C>T		intron_variant	Intron 1 of 2
ENSG00000305096	ENST00000808499.1	n.144+1424C>T		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.587 AC: 89092 AN: 151776 Hom.: 27273 Cov.: 31

Gnomad AFR AF: 0.415

Gnomad AMI AF: 0.759

Gnomad AMR AF: 0.664

Gnomad ASJ AF: 0.757

Gnomad EAS AF: 0.444

Gnomad SAS AF: 0.489

Gnomad FIN AF: 0.642

Gnomad MID AF: 0.642

Gnomad NFE AF: 0.671

Gnomad OTH AF: 0.617

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

GnomAD4 genome AF: 0.587 AC: 89166 AN: 151894 Hom.: 27295 Cov.: 31 AF XY: 0.585 AC XY: 43445 AN XY: 74228

African (AFR) AF: 0.416 AC: 17194 AN: 41366

American (AMR) AF: 0.664 AC: 10150 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.757 AC: 2624 AN: 3468

East Asian (EAS) AF: 0.444 AC: 2299 AN: 5174

South Asian (SAS) AF: 0.488 AC: 2351 AN: 4814

European-Finnish (FIN) AF: 0.642 AC: 6769 AN: 10538

Middle Eastern (MID) AF: 0.650 AC: 191 AN: 294

European-Non Finnish (NFE) AF: 0.671 AC: 45602 AN: 67950

Other (OTH) AF: 0.616 AC: 1298 AN: 2108

Alfa AF: 0.644 Hom.: 130636

Bravo AF: 0.579

Asia WGS AF: 0.443 AC: 1543 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.1
DANN	Benign	0.50
PhyloP100		-0.046

Splicing

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

Other links and lift over

dbSNP: rs4430311; hg19: chr1-244015993;