rs1365057

Variant names:

• chr11-35088128-G-A
• rs1365057
• ENST00000748002.1:n.441G>A

Your query was ambiguous. Multiple possible variants found:

• chr11-35088128-G-A
• chr11-35088128-G-C
• chr11-35088128-G-T

Variant summary

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

The ENST00000748002.1(ENSG00000297460):​n.441G>A 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 0.242 in 152,150 control chromosomes in the GnomAD database, including 4,636 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 0.24 (4636 hom., cov: 32)
• Consequence: ENSG00000297460 ENST00000748002.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.891
• Publications: 10 publications found

Genes affected

ENSG00000297460 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.378 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105376627	XR_001748184.2	n.99G>A		non_coding_transcript_exon_variant	Exon 1 of 3
LOC105376627	XR_931193.3	n.99G>A		non_coding_transcript_exon_variant	Exon 1 of 4
LOC105376627	XR_931194.2	n.4055-310G>A		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000297460	ENST00000748002.1	n.441G>A		non_coding_transcript_exon_variant	Exon 1 of 3
ENSG00000297460	ENST00000748003.1	n.107G>A		non_coding_transcript_exon_variant	Exon 1 of 4
ENSG00000297460	ENST00000747995.1	n.137-310G>A		intron_variant	Intron 2 of 4

Frequencies

GnomAD3 genomes AF: 0.243 AC: 36873 AN: 152032 Hom.: 4648 Cov.: 32

Gnomad AFR AF: 0.229

Gnomad AMI AF: 0.277

Gnomad AMR AF: 0.285

Gnomad ASJ AF: 0.310

Gnomad EAS AF: 0.393

Gnomad SAS AF: 0.156

Gnomad FIN AF: 0.254

Gnomad MID AF: 0.244

Gnomad NFE AF: 0.230

Gnomad OTH AF: 0.248

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

GnomAD4 genome AF: 0.242 AC: 36871 AN: 152150 Hom.: 4636 Cov.: 32 AF XY: 0.242 AC XY: 17996 AN XY: 74392

African (AFR) AF: 0.229 AC: 9515 AN: 41504

American (AMR) AF: 0.285 AC: 4354 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.310 AC: 1075 AN: 3468

East Asian (EAS) AF: 0.392 AC: 2034 AN: 5186

South Asian (SAS) AF: 0.155 AC: 747 AN: 4822

European-Finnish (FIN) AF: 0.254 AC: 2687 AN: 10570

Middle Eastern (MID) AF: 0.245 AC: 72 AN: 294

European-Non Finnish (NFE) AF: 0.230 AC: 15618 AN: 67990

Other (OTH) AF: 0.245 AC: 517 AN: 2112

Alfa AF: 0.234 Hom.: 18079

Bravo AF: 0.246

Asia WGS AF: 0.292 AC: 1014 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.7
DANN	Benign	0.59
PhyloP100		-0.89

Splicing

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

Other links and lift over

dbSNP: rs1365057; hg19: chr11-35109675;