chr1-11262852-G-T

Variant names:

• chr1-11262852-G-T
• rs17027478
• ENST00000838067.1:n.74G>T

Variant summary

Our verdict is Benign. The variant received -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The ENST00000838067.1(ENSG00000309051):​n.74G>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0308 in 152,230 control chromosomes in the GnomAD database, including 194 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.031 (194 hom., cov: 31)
• Consequence: ENSG00000309051 ENST00000838067.1 non_coding_transcript_exon
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.736
• Publications: 2 publications found

Genes affected

ENSG00000309051 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BP6: Variant 1-11262852-G-T is Benign according to our data. Variant chr1-11262852-G-T is described in ClinVar as Benign. ClinVar VariationId is 1167316.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0704 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
ENSG00000309051	ENST00000838067.1	n.74G>T		non_coding_transcript_exon_variant	Exon 1 of 2

Frequencies

GnomAD3 genomes AF: 0.0307 AC: 4667 AN: 152112 Hom.: 189 Cov.: 31

Gnomad AFR AF: 0.0722

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0711

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.0449

Gnomad SAS AF: 0.0583

Gnomad FIN AF: 0.000188

Gnomad MID AF: 0.00949

Gnomad NFE AF: 0.000397

Gnomad OTH AF: 0.0229

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

GnomAD4 genome AF: 0.0308 AC: 4690 AN: 152230 Hom.: 194 Cov.: 31 AF XY: 0.0325 AC XY: 2420 AN XY: 74440

African (AFR) AF: 0.0726 AC: 3011 AN: 41500

American (AMR) AF: 0.0711 AC: 1087 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3472

East Asian (EAS) AF: 0.0450 AC: 233 AN: 5182

South Asian (SAS) AF: 0.0578 AC: 279 AN: 4830

European-Finnish (FIN) AF: 0.000188 AC: 2 AN: 10618

Middle Eastern (MID) AF: 0.0102 AC: 3 AN: 294

European-Non Finnish (NFE) AF: 0.000397 AC: 27 AN: 68024

Other (OTH) AF: 0.0227 AC: 48 AN: 2116

Alfa AF: 0.0226 Hom.: 6

Bravo AF: 0.0361

Asia WGS AF: 0.0610 AC: 215 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Jan 06, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

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Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	7.3
DANN	Benign	0.76
PhyloP100		0.74
PromoterAI		0.063	Neutral

Splicing

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

Other links and lift over

dbSNP: rs17027478; hg19: chr1-11322909;