1-100711577-G-T

Variant names:

• chr1-100711577-G-T
• rs1582091
• ENST00000762830.1:n.155-13016C>A

Variant summary

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

The ENST00000762830.1(ENSG00000299357):​n.155-13016C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.559 in 151,798 control chromosomes in the GnomAD database, including 24,430 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 0.56 (24430 hom., cov: 31)
• Consequence: ENSG00000299357 ENST00000762830.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.408
• Publications: 4 publications found

Genes affected

ENSG00000299357 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.657 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
ENSG00000299357	ENST00000762830.1	n.155-13016C>A		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.559 AC: 84724 AN: 151680 Hom.: 24393 Cov.: 31

Gnomad AFR AF: 0.663

Gnomad AMI AF: 0.587

Gnomad AMR AF: 0.645

Gnomad ASJ AF: 0.555

Gnomad EAS AF: 0.433

Gnomad SAS AF: 0.559

Gnomad FIN AF: 0.502

Gnomad MID AF: 0.570

Gnomad NFE AF: 0.494

Gnomad OTH AF: 0.568

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

GnomAD4 genome AF: 0.559 AC: 84811 AN: 151798 Hom.: 24430 Cov.: 31 AF XY: 0.561 AC XY: 41623 AN XY: 74156

African (AFR) AF: 0.663 AC: 27454 AN: 41402

American (AMR) AF: 0.646 AC: 9847 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.555 AC: 1924 AN: 3468

East Asian (EAS) AF: 0.433 AC: 2227 AN: 5148

South Asian (SAS) AF: 0.558 AC: 2680 AN: 4804

European-Finnish (FIN) AF: 0.502 AC: 5283 AN: 10524

Middle Eastern (MID) AF: 0.558 AC: 164 AN: 294

European-Non Finnish (NFE) AF: 0.494 AC: 33507 AN: 67888

Other (OTH) AF: 0.564 AC: 1190 AN: 2110

Alfa AF: 0.493 Hom.: 4597

Bravo AF: 0.577

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.9
DANN	Benign	0.32
PhyloP100		0.41

Splicing

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

Other links and lift over

dbSNP: rs1582091; hg19: chr1-101177133;