rs10504862

Positions:

• chr8-88535666-A-T

Variant summary

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

The ENST00000665922.1(ENSG00000253553):​n.194-7014A>T 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 0.371 in 151,928 control chromosomes in the GnomAD database, including 11,820 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 0.37 (11820 hom., cov: 32)
• Consequence: ENST00000665922.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.838

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.567 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105375630	XR_001745653.3	n.225-7014A>T		intron_variant, non_coding_transcript_variant
LOC105375629	XR_928383.4	n.478+10851T>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000665922.1	n.194-7014A>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.371 AC: 56299 AN: 151810 Hom.: 11772 Cov.: 32

Gnomad AFR AF: 0.573

Gnomad AMI AF: 0.322

Gnomad AMR AF: 0.328

Gnomad ASJ AF: 0.245

Gnomad EAS AF: 0.170

Gnomad SAS AF: 0.439

Gnomad FIN AF: 0.288

Gnomad MID AF: 0.325

Gnomad NFE AF: 0.288

Gnomad OTH AF: 0.371

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

GnomAD4 genome AF: 0.371 AC: 56402 AN: 151928 Hom.: 11820 Cov.: 32 AF XY: 0.372 AC XY: 27647 AN XY: 74234

Gnomad4 AFR AF: 0.573

Gnomad4 AMR AF: 0.328

Gnomad4 ASJ AF: 0.245

Gnomad4 EAS AF: 0.170

Gnomad4 SAS AF: 0.437

Gnomad4 FIN AF: 0.288

Gnomad4 NFE AF: 0.288

Gnomad4 OTH AF: 0.376

Alfa AF: 0.343 Hom.: 1195

Bravo AF: 0.378

Asia WGS AF: 0.374 AC: 1298 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.9
DANN	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10504862; hg19: chr8-89547895;