rs11595808

Variant names:

• chr10-46193242-C-A
• rs11595808
• XR_007062137.1:n.9832G>T

Variant summary

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

The XR_007062137.1(LOC124902418):​n.9832G>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 0.0165 in 151,784 control chromosomes in the GnomAD database, including 45 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 0.016 (45 hom., cov: 32)
• Consequence: LOC124902418 XR_007062137.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.28
• Publications: 1 publications found

Genes affected

LOC124902418 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BS1: Variant frequency is greater than expected in population amr. GnomAd4 allele frequency = 0.0165 (2499/151784) while in subpopulation AMR AF = 0.0284 (433/15238). AF 95% confidence interval is 0.0262. There are 45 homozygotes in GnomAd4. There are 1209 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 45 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124902418	XR_007062137.1	n.9832G>T		non_coding_transcript_exon_variant	Exon 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000299562	ENST00000764651.1	n.127-45276G>T		intron_variant	Intron 1 of 2
ENSG00000299562	ENST00000764652.1	n.150+9309G>T		intron_variant	Intron 2 of 3
ENSG00000299562	ENST00000764653.1	n.78+11208G>T		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.0165 AC: 2499 AN: 151666 Hom.: 44 Cov.: 32

Gnomad AFR AF: 0.00411

Gnomad AMI AF: 0.0406

Gnomad AMR AF: 0.0283

Gnomad ASJ AF: 0.0245

Gnomad EAS AF: 0.0191

Gnomad SAS AF: 0.0181

Gnomad FIN AF: 0.0178

Gnomad MID AF: 0.0127

Gnomad NFE AF: 0.0200

Gnomad OTH AF: 0.0187

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

GnomAD4 genome AF: 0.0165 AC: 2499 AN: 151784 Hom.: 45 Cov.: 32 AF XY: 0.0163 AC XY: 1209 AN XY: 74236

African (AFR) AF: 0.00410 AC: 169 AN: 41206

American (AMR) AF: 0.0284 AC: 433 AN: 15238

Ashkenazi Jewish (ASJ) AF: 0.0245 AC: 85 AN: 3470

East Asian (EAS) AF: 0.0189 AC: 98 AN: 5174

South Asian (SAS) AF: 0.0181 AC: 87 AN: 4810

European-Finnish (FIN) AF: 0.0178 AC: 189 AN: 10602

Middle Eastern (MID) AF: 0.0102 AC: 3 AN: 294

European-Non Finnish (NFE) AF: 0.0200 AC: 1359 AN: 67974

Other (OTH) AF: 0.0185 AC: 39 AN: 2104

Alfa AF: 0.0183 Hom.: 3

Bravo AF: 0.0171

Asia WGS AF: 0.0290 AC: 100 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.76
DANN	Benign	0.54
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs11595808; hg19: chr10-47564478;