XR_007062110.1:n.96G>C

Variant names:

• chr10-35006503-C-G
• rs11010067
• XR_007062110.1:n.96G>C

Variant summary

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

The XR_007062110.1(LOC124902409):​n.96G>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 0.366 in 152,018 control chromosomes in the GnomAD database, including 10,275 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 0.37 (10275 hom., cov: 32)
• Consequence: LOC124902409 XR_007062110.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.38
• Publications: 54 publications found

Genes affected

LOC124902409 (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 = 0.408 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124902409	XR_007062110.1	n.96G>C		non_coding_transcript_exon_variant	Exon 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000301061	ENST00000775934.1	n.64-3750C>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.366 AC: 55531 AN: 151900 Hom.: 10246 Cov.: 32

Gnomad AFR AF: 0.412

Gnomad AMI AF: 0.258

Gnomad AMR AF: 0.324

Gnomad ASJ AF: 0.400

Gnomad EAS AF: 0.318

Gnomad SAS AF: 0.347

Gnomad FIN AF: 0.390

Gnomad MID AF: 0.329

Gnomad NFE AF: 0.347

Gnomad OTH AF: 0.366

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

GnomAD4 genome AF: 0.366 AC: 55621 AN: 152018 Hom.: 10275 Cov.: 32 AF XY: 0.365 AC XY: 27141 AN XY: 74318

African (AFR) AF: 0.413 AC: 17126 AN: 41480

American (AMR) AF: 0.325 AC: 4951 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.400 AC: 1387 AN: 3468

East Asian (EAS) AF: 0.318 AC: 1642 AN: 5168

South Asian (SAS) AF: 0.347 AC: 1671 AN: 4810

European-Finnish (FIN) AF: 0.390 AC: 4112 AN: 10540

Middle Eastern (MID) AF: 0.327 AC: 96 AN: 294

European-Non Finnish (NFE) AF: 0.347 AC: 23616 AN: 67982

Other (OTH) AF: 0.372 AC: 785 AN: 2108

Alfa AF: 0.353 Hom.: 1210

Bravo AF: 0.362

Asia WGS AF: 0.366 AC: 1271 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	0.22
DANN	Benign	0.52
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs11010067; hg19: chr10-35295431;