rs10498966

Variant names:

• chr6-90322375-A-G
• rs10498966
• ENST00000650187.1:n.59+1874A>G

Variant summary

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

The ENST00000650187.1(ENSG00000260271):​n.59+1874A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0424 in 152,192 control chromosomes in the GnomAD database, including 174 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 0.042 (174 hom., cov: 30)
• Consequence: ENSG00000260271 ENST00000650187.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.274
• Publications: 2 publications found

Genes affected

ENSG00000260271 (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 (SAS) allele frequency at 95% confidence interval = 0.108 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105377891	XR_007059677.1	n.499-22846A>G		intron_variant	Intron 1 of 4
LOC105377891	XR_942778.4	n.499-8989A>G		intron_variant	Intron 1 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000260271	ENST00000650187.1	n.59+1874A>G		intron_variant	Intron 1 of 8
ENSG00000260271	ENST00000654016.1	n.44-8989A>G		intron_variant	Intron 1 of 7
ENSG00000260271	ENST00000663503.1	n.86-8989A>G		intron_variant	Intron 1 of 4

Frequencies

GnomAD3 genomes AF: 0.0425 AC: 6461 AN: 152074 Hom.: 175 Cov.: 30

Gnomad AFR AF: 0.0532

Gnomad AMI AF: 0.0998

Gnomad AMR AF: 0.0282

Gnomad ASJ AF: 0.108

Gnomad EAS AF: 0.00192

Gnomad SAS AF: 0.116

Gnomad FIN AF: 0.0208

Gnomad MID AF: 0.0443

Gnomad NFE AF: 0.0361

Gnomad OTH AF: 0.0483

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

GnomAD4 genome AF: 0.0424 AC: 6460 AN: 152192 Hom.: 174 Cov.: 30 AF XY: 0.0417 AC XY: 3102 AN XY: 74390

African (AFR) AF: 0.0532 AC: 2209 AN: 41508

American (AMR) AF: 0.0282 AC: 431 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.108 AC: 375 AN: 3470

East Asian (EAS) AF: 0.00193 AC: 10 AN: 5192

South Asian (SAS) AF: 0.116 AC: 556 AN: 4812

European-Finnish (FIN) AF: 0.0208 AC: 221 AN: 10604

Middle Eastern (MID) AF: 0.0408 AC: 12 AN: 294

European-Non Finnish (NFE) AF: 0.0361 AC: 2455 AN: 68000

Other (OTH) AF: 0.0473 AC: 100 AN: 2112

Alfa AF: 0.0445 Hom.: 60

Bravo AF: 0.0419

Asia WGS AF: 0.0510 AC: 176 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	5.0
DANN	Benign	0.76
PhyloP100		0.27

Splicing

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

Other links and lift over

dbSNP: rs10498966; hg19: chr6-91032094;