rs10098562

Positions:

• chr8-108940833-G-A

Variant summary

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

The ENST00000522244.1(ENSG00000253796):​n.265-22187C>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 0.114 in 152,028 control chromosomes in the GnomAD database, including 2,056 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 0.11 (2056 hom., cov: 31)
• Consequence: ENST00000522244.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.181

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.296 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC101927413	XR_928533.3	n.134+7942C>T		intron_variant, non_coding_transcript_variant
LOC101927413	XR_242419.4	n.134+7942C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000522244.1	n.265-22187C>T		intron_variant, non_coding_transcript_variant		3
	ENST00000656015.3	n.138+7942C>T		intron_variant, non_coding_transcript_variant
	ENST00000702172.1	n.134+7942C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.114 AC: 17245 AN: 151910 Hom.: 2049 Cov.: 31

Gnomad AFR AF: 0.300

Gnomad AMI AF: 0.00439

Gnomad AMR AF: 0.0614

Gnomad ASJ AF: 0.0210

Gnomad EAS AF: 0.000772

Gnomad SAS AF: 0.140

Gnomad FIN AF: 0.0536

Gnomad MID AF: 0.0981

Gnomad NFE AF: 0.0345

Gnomad OTH AF: 0.0971

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

GnomAD4 genome AF: 0.114 AC: 17285 AN: 152028 Hom.: 2056 Cov.: 31 AF XY: 0.115 AC XY: 8535 AN XY: 74312

Gnomad4 AFR AF: 0.300

Gnomad4 AMR AF: 0.0613

Gnomad4 ASJ AF: 0.0210

Gnomad4 EAS AF: 0.000773

Gnomad4 SAS AF: 0.141

Gnomad4 FIN AF: 0.0536

Gnomad4 NFE AF: 0.0346

Gnomad4 OTH AF: 0.0999

Alfa AF: 0.0794 Hom.: 190

Bravo AF: 0.119

Asia WGS AF: 0.0900 AC: 313 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	9.6
DANN	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10098562; hg19: chr8-109953062;