chr1-96034274-T-A

Variant names:

• chr1-96034274-T-A
• rs161115
• ENST00000766019.1:n.72+4153A>T

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

The ENST00000766019.1(ENSG00000299748):​n.72+4153A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.388 in 151,606 control chromosomes in the GnomAD database, including 11,811 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.39 (11811 hom., cov: 32)
• Consequence: ENSG00000299748 ENST00000766019.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.90
• Publications: 13 publications found

Genes affected

ENSG00000299748 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.47 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
ENSG00000299748	ENST00000766019.1	n.72+4153A>T		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.388 AC: 58852 AN: 151486 Hom.: 11801 Cov.: 32

Gnomad AFR AF: 0.295

Gnomad AMI AF: 0.391

Gnomad AMR AF: 0.478

Gnomad ASJ AF: 0.400

Gnomad EAS AF: 0.459

Gnomad SAS AF: 0.397

Gnomad FIN AF: 0.369

Gnomad MID AF: 0.299

Gnomad NFE AF: 0.422

Gnomad OTH AF: 0.385

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

GnomAD4 genome AF: 0.388 AC: 58886 AN: 151606 Hom.: 11811 Cov.: 32 AF XY: 0.387 AC XY: 28645 AN XY: 74088

African (AFR) AF: 0.294 AC: 12158 AN: 41344

American (AMR) AF: 0.479 AC: 7287 AN: 15218

Ashkenazi Jewish (ASJ) AF: 0.400 AC: 1383 AN: 3460

East Asian (EAS) AF: 0.460 AC: 2376 AN: 5168

South Asian (SAS) AF: 0.398 AC: 1918 AN: 4822

European-Finnish (FIN) AF: 0.369 AC: 3896 AN: 10570

Middle Eastern (MID) AF: 0.298 AC: 87 AN: 292

European-Non Finnish (NFE) AF: 0.422 AC: 28610 AN: 67718

Other (OTH) AF: 0.387 AC: 814 AN: 2102

Alfa AF: 0.386 Hom.: 1459

Bravo AF: 0.393

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Uncertain	-0.080
CADD	Benign	19
DANN	Benign	0.79
PhyloP100		1.9

Splicing

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

Other links and lift over

dbSNP: rs161115; hg19: chr1-96499830;