rs10488089

Variant names:

• chr7-30223744-C-G
• rs10488089
• XR_007060273.1:n.35217C>G

Your query was ambiguous. Multiple possible variants found:

• chr7-30223744-C-G
• chr7-30223744-C-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The XR_007060273.1(LOC124901607):​n.35217C>G 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 0.02 in 152,256 control chromosomes in the GnomAD database, including 50 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 0.020 (50 hom., cov: 33)
• Consequence: LOC124901607 XR_007060273.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.30
• Publications: 2 publications found

Genes affected

LOC124901607 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BS1: Variant frequency is greater than expected in population nfe. GnomAd4 allele frequency = 0.02 (3038/152256) while in subpopulation NFE AF = 0.031 (2108/68026). AF 95% confidence interval is 0.0299. There are 50 homozygotes in GnomAd4. There are 1350 alleles in the male GnomAd4 subpopulation. Median coverage is 33. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 50 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124901607	XR_007060273.1	n.35217C>G		non_coding_transcript_exon_variant	Exon 1 of 3
LOC124901607	XR_007060274.1	n.21081-3906C>G		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0200 AC: 3039 AN: 152138 Hom.: 50 Cov.: 33

Gnomad AFR AF: 0.00584

Gnomad AMI AF: 0.114

Gnomad AMR AF: 0.0215

Gnomad ASJ AF: 0.0236

Gnomad EAS AF: 0.000192

Gnomad SAS AF: 0.00808

Gnomad FIN AF: 0.00698

Gnomad MID AF: 0.0190

Gnomad NFE AF: 0.0310

Gnomad OTH AF: 0.0263

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

GnomAD4 genome AF: 0.0200 AC: 3038 AN: 152256 Hom.: 50 Cov.: 33 AF XY: 0.0181 AC XY: 1350 AN XY: 74442

African (AFR) AF: 0.00582 AC: 242 AN: 41546

American (AMR) AF: 0.0215 AC: 328 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.0236 AC: 82 AN: 3470

East Asian (EAS) AF: 0.000193 AC: 1 AN: 5190

South Asian (SAS) AF: 0.00809 AC: 39 AN: 4822

European-Finnish (FIN) AF: 0.00698 AC: 74 AN: 10596

Middle Eastern (MID) AF: 0.0204 AC: 6 AN: 294

European-Non Finnish (NFE) AF: 0.0310 AC: 2108 AN: 68026

Other (OTH) AF: 0.0255 AC: 54 AN: 2116

Alfa AF: 0.00468 Hom.: 3

Bravo AF: 0.0204

Asia WGS AF: 0.00549 AC: 19 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.021
DANN	Benign	0.59
PhyloP100		-2.3

Splicing

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

Other links and lift over

dbSNP: rs10488089; hg19: chr7-30263360;