XR_007062655.1:n.180T>C

Variant names:

• chr11-35892021-T-C
• rs16928055
• XR_007062655.1:n.180T>C

Variant summary

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

The XR_007062655.1(LOC124902661):​n.180T>C 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 0.103 in 152,266 control chromosomes in the GnomAD database, including 1,103 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 (1103 hom., cov: 32)
• Consequence: LOC124902661 XR_007062655.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0400
• Publications: 0 publications found

Genes affected

LOC124902661 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.236 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124902661	XR_007062655.1	n.180T>C		non_coding_transcript_exon_variant	Exon 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000254919	ENST00000730429.1	n.264+25990A>G		intron_variant	Intron 2 of 3
ENSG00000254919	ENST00000730430.1	n.268+25990A>G		intron_variant	Intron 2 of 3
ENSG00000254919	ENST00000730431.1	n.265+25990A>G		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.103 AC: 15614 AN: 152148 Hom.: 1102 Cov.: 32

Gnomad AFR AF: 0.0242

Gnomad AMI AF: 0.280

Gnomad AMR AF: 0.132

Gnomad ASJ AF: 0.147

Gnomad EAS AF: 0.248

Gnomad SAS AF: 0.213

Gnomad FIN AF: 0.104

Gnomad MID AF: 0.136

Gnomad NFE AF: 0.119

Gnomad OTH AF: 0.116

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

GnomAD4 genome AF: 0.103 AC: 15618 AN: 152266 Hom.: 1103 Cov.: 32 AF XY: 0.106 AC XY: 7860 AN XY: 74440

African (AFR) AF: 0.0241 AC: 1002 AN: 41576

American (AMR) AF: 0.132 AC: 2021 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.147 AC: 511 AN: 3472

East Asian (EAS) AF: 0.248 AC: 1283 AN: 5182

South Asian (SAS) AF: 0.212 AC: 1023 AN: 4818

European-Finnish (FIN) AF: 0.104 AC: 1102 AN: 10596

Middle Eastern (MID) AF: 0.136 AC: 40 AN: 294

European-Non Finnish (NFE) AF: 0.119 AC: 8121 AN: 68012

Other (OTH) AF: 0.123 AC: 260 AN: 2112

Alfa AF: 0.120 Hom.: 2337

Bravo AF: 0.102

Asia WGS AF: 0.220 AC: 762 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.2
DANN	Benign	0.33
PhyloP100		-0.040

Splicing

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

Other links and lift over

dbSNP: rs16928055; hg19: chr11-35913571;