rs10498966

chr6-90322375-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000667364.1(ENSG00000260271):n.31-22846A>G variant causes a intron, non coding transcript 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: ENST00000667364.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.274

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
LOC105377891	XR_942778.4	n.499-8989A>G		intron_variant, non_coding_transcript_variant
LOC105377891	XR_007059677.1	n.499-22846A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000667364.1	n.31-22846A>G		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.0532

Gnomad4 AMR AF: 0.0282

Gnomad4 ASJ AF: 0.108

Gnomad4 EAS AF: 0.00193

Gnomad4 SAS AF: 0.116

Gnomad4 FIN AF: 0.0208

Gnomad4 NFE AF: 0.0361

Gnomad4 OTH AF: 0.0473

Alfa AF: 0.0376 Hom.: 13

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10498966; hg19: chr6-91032094;