chr1-65733540-C-T

Variant names:

• chr1-65733540-C-T
• rs5010905
• ENST00000760442.1:n.343-12851G>A

Variant summary

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

The ENST00000760442.1(ENSG00000299098):​n.343-12851G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.75 in 152,132 control chromosomes in the GnomAD database, including 42,798 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 0.75 (42798 hom., cov: 32)
• Consequence: ENSG00000299098 ENST00000760442.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.07
• Publications: 7 publications found

Genes affected

ENSG00000299098 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 = 0.896 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
ENSG00000299098	ENST00000760442.1	n.343-12851G>A		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.750 AC: 113988 AN: 152014 Hom.: 42765 Cov.: 32

Gnomad AFR AF: 0.722

Gnomad AMI AF: 0.682

Gnomad AMR AF: 0.803

Gnomad ASJ AF: 0.754

Gnomad EAS AF: 0.917

Gnomad SAS AF: 0.767

Gnomad FIN AF: 0.759

Gnomad MID AF: 0.775

Gnomad NFE AF: 0.739

Gnomad OTH AF: 0.772

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

GnomAD4 genome AF: 0.750 AC: 114076 AN: 152132 Hom.: 42798 Cov.: 32 AF XY: 0.753 AC XY: 55963 AN XY: 74366

African (AFR) AF: 0.722 AC: 29947 AN: 41468

American (AMR) AF: 0.804 AC: 12292 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.754 AC: 2617 AN: 3472

East Asian (EAS) AF: 0.918 AC: 4746 AN: 5172

South Asian (SAS) AF: 0.766 AC: 3696 AN: 4824

European-Finnish (FIN) AF: 0.759 AC: 8029 AN: 10578

Middle Eastern (MID) AF: 0.769 AC: 226 AN: 294

European-Non Finnish (NFE) AF: 0.739 AC: 50270 AN: 68008

Other (OTH) AF: 0.773 AC: 1632 AN: 2112

Alfa AF: 0.745 Hom.: 31157

Bravo AF: 0.749

Asia WGS AF: 0.843 AC: 2930 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	2.1
DANN	Benign	0.40
PhyloP100		1.1

Splicing

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

Other links and lift over

dbSNP: rs5010905; hg19: chr1-66199223;