rs10499094

Variant names:

• chr6-119800707-A-G
• rs10499094
• NR_134600.1:n.253-42359A>G

Variant summary

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

The NR_134600.1(LOC105377975):​n.253-42359A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.195 in 152,066 control chromosomes in the GnomAD database, including 3,069 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 0.19 (3069 hom., cov: 32)
• Consequence: LOC105377975 NR_134600.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.183
• Publications: 1 publications found

Genes affected

LOC105377975 (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 (NFE) allele frequency at 95% confidence interval = 0.22 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105377975	NR_134600.1	n.253-42359A>G		intron_variant	Intron 2 of 3

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.195 AC: 29570 AN: 151948 Hom.: 3067 Cov.: 32

Gnomad AFR AF: 0.175

Gnomad AMI AF: 0.368

Gnomad AMR AF: 0.171

Gnomad ASJ AF: 0.254

Gnomad EAS AF: 0.114

Gnomad SAS AF: 0.103

Gnomad FIN AF: 0.165

Gnomad MID AF: 0.256

Gnomad NFE AF: 0.223

Gnomad OTH AF: 0.191

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

GnomAD4 genome AF: 0.195 AC: 29581 AN: 152066 Hom.: 3069 Cov.: 32 AF XY: 0.190 AC XY: 14154 AN XY: 74354

African (AFR) AF: 0.175 AC: 7271 AN: 41478

American (AMR) AF: 0.171 AC: 2610 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.254 AC: 883 AN: 3472

East Asian (EAS) AF: 0.113 AC: 587 AN: 5182

South Asian (SAS) AF: 0.103 AC: 499 AN: 4826

European-Finnish (FIN) AF: 0.165 AC: 1743 AN: 10588

Middle Eastern (MID) AF: 0.265 AC: 78 AN: 294

European-Non Finnish (NFE) AF: 0.223 AC: 15175 AN: 67952

Other (OTH) AF: 0.190 AC: 401 AN: 2110

Alfa AF: 0.211 Hom.: 1793

Bravo AF: 0.196

Asia WGS AF: 0.131 AC: 459 AN: 3474

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	0.67
PhyloP100		0.18

Splicing

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

Other links and lift over

dbSNP: rs10499094; hg19: chr6-120121853;