rs10498690

Variant names:

• chr6-18498116-G-A
• rs10498690
• XR_926548.3:n.147+1110G>A

Your query was ambiguous. Multiple possible variants found:

• chr6-18498116-G-A
• chr6-18498116-G-T

Variant summary

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

The XR_926548.3(LOC105374955):​n.147+1110G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0352 in 152,266 control chromosomes in the GnomAD database, including 105 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 0.035 (105 hom., cov: 33)
• Consequence: LOC105374955 XR_926548.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.276
• Publications: 1 publications found

Genes affected

LOC105374955 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BS1: Variant frequency is greater than expected in population nfe. GnomAd4 allele frequency = 0.0352 (5357/152266) while in subpopulation NFE AF = 0.0461 (3136/68022). AF 95% confidence interval is 0.0448. There are 105 homozygotes in GnomAd4. There are 2602 alleles in the male GnomAd4 subpopulation. Median coverage is 33. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 105 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105374955	XR_926548.3	n.147+1110G>A		intron_variant	Intron 1 of 3
LOC105374955	XR_926549.3	n.147+1110G>A		intron_variant	Intron 1 of 3

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0352 AC: 5360 AN: 152150 Hom.: 105 Cov.: 33

Gnomad AFR AF: 0.0175

Gnomad AMI AF: 0.0208

Gnomad AMR AF: 0.0436

Gnomad ASJ AF: 0.0424

Gnomad EAS AF: 0.000963

Gnomad SAS AF: 0.0342

Gnomad FIN AF: 0.0380

Gnomad MID AF: 0.0190

Gnomad NFE AF: 0.0461

Gnomad OTH AF: 0.0416

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

GnomAD4 genome AF: 0.0352 AC: 5357 AN: 152266 Hom.: 105 Cov.: 33 AF XY: 0.0350 AC XY: 2602 AN XY: 74444

African (AFR) AF: 0.0174 AC: 724 AN: 41558

American (AMR) AF: 0.0435 AC: 666 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0424 AC: 147 AN: 3470

East Asian (EAS) AF: 0.000965 AC: 5 AN: 5180

South Asian (SAS) AF: 0.0342 AC: 165 AN: 4824

European-Finnish (FIN) AF: 0.0380 AC: 403 AN: 10598

Middle Eastern (MID) AF: 0.0170 AC: 5 AN: 294

European-Non Finnish (NFE) AF: 0.0461 AC: 3136 AN: 68022

Other (OTH) AF: 0.0412 AC: 87 AN: 2112

Alfa AF: 0.0424 Hom.: 59

Bravo AF: 0.0347

Asia WGS AF: 0.0190 AC: 65 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	0.56
DANN	Benign	0.81
PhyloP100		-0.28

Splicing

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

Other links and lift over

dbSNP: rs10498690; hg19: chr6-18498347;