rs10491074

chr10-64058802-A-G

Variant summary

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

The ENST00000654191.1(ENSG00000228566):n.517-1324A>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 0.0761 in 152,226 control chromosomes in the GnomAD database, including 940 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 0.076 (940 hom., cov: 32)
• Consequence: ENST00000654191.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.675

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.199 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124902439	XR_007062161.1	n.498-1324A>G		intron_variant, non_coding_transcript_variant
LOC124902439	XR_007062160.1	n.496-1324A>G		intron_variant, non_coding_transcript_variant
LOC124902439	XR_007062163.1	n.175-1324A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000654191.1	n.517-1324A>G		intron_variant, non_coding_transcript_variant
	ENST00000660795.1	n.266-1324A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0759 AC: 11546 AN: 152108 Hom.: 936 Cov.: 32

Gnomad AFR AF: 0.202

Gnomad AMI AF: 0.0329

Gnomad AMR AF: 0.0648

Gnomad ASJ AF: 0.0499

Gnomad EAS AF: 0.0256

Gnomad SAS AF: 0.0319

Gnomad FIN AF: 0.00528

Gnomad MID AF: 0.0886

Gnomad NFE AF: 0.0216

Gnomad OTH AF: 0.0717

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

GnomAD4 genome AF: 0.0761 AC: 11583 AN: 152226 Hom.: 940 Cov.: 32 AF XY: 0.0739 AC XY: 5502 AN XY: 74428

Gnomad4 AFR AF: 0.202

Gnomad4 AMR AF: 0.0650

Gnomad4 ASJ AF: 0.0499

Gnomad4 EAS AF: 0.0259

Gnomad4 SAS AF: 0.0311

Gnomad4 FIN AF: 0.00528

Gnomad4 NFE AF: 0.0216

Gnomad4 OTH AF: 0.0714

Alfa AF: 0.0503 Hom.: 82

Bravo AF: 0.0883

Asia WGS AF: 0.0470 AC: 162 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
Cadd	Benign	9.9
Dann	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10491074; hg19: chr10-65818562;