rs11265608

Variant names:

• chr1-154391664-G-A
• rs11265608
• ENST00000745818.1:n.434C>T

Variant summary

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

The ENST00000745818.1(ENSG00000297143):​n.434C>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 0.1 in 152,194 control chromosomes in the GnomAD database, including 816 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 0.10 (816 hom., cov: 32)
• Consequence: ENSG00000297143 ENST00000745818.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.603
• Publications: 27 publications found

Genes affected

ENSG00000297143 (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 (AFR) allele frequency at 95% confidence interval = 0.12 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
ENSG00000297143	ENST00000745818.1	n.434C>T		non_coding_transcript_exon_variant	Exon 2 of 2
ENSG00000297143	ENST00000745819.1	n.272C>T		non_coding_transcript_exon_variant	Exon 2 of 2
ENSG00000297143	ENST00000745817.1	n.212-8286C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.0999 AC: 15191 AN: 152076 Hom.: 811 Cov.: 32

Gnomad AFR AF: 0.122

Gnomad AMI AF: 0.0735

Gnomad AMR AF: 0.0602

Gnomad ASJ AF: 0.103

Gnomad EAS AF: 0.0367

Gnomad SAS AF: 0.0433

Gnomad FIN AF: 0.136

Gnomad MID AF: 0.0475

Gnomad NFE AF: 0.0995

Gnomad OTH AF: 0.0834

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

GnomAD4 genome AF: 0.100 AC: 15221 AN: 152194 Hom.: 816 Cov.: 32 AF XY: 0.101 AC XY: 7504 AN XY: 74384

African (AFR) AF: 0.122 AC: 5083 AN: 41542

American (AMR) AF: 0.0601 AC: 918 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.103 AC: 358 AN: 3472

East Asian (EAS) AF: 0.0368 AC: 191 AN: 5186

South Asian (SAS) AF: 0.0429 AC: 207 AN: 4820

European-Finnish (FIN) AF: 0.136 AC: 1437 AN: 10580

Middle Eastern (MID) AF: 0.0442 AC: 13 AN: 294

European-Non Finnish (NFE) AF: 0.0995 AC: 6766 AN: 68004

Other (OTH) AF: 0.0859 AC: 181 AN: 2108

Alfa AF: 0.0963 Hom.: 617

Bravo AF: 0.0938

Asia WGS AF: 0.0660 AC: 231 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	3.4
DANN	Benign	0.33
PhyloP100		0.60

Splicing

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

Other links and lift over

dbSNP: rs11265608; hg19: chr1-154364140;