rs10104895

Positions:

• chr8-60963485-G-A
• chr8-60963485-G-C

Variant summary

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

The ENST00000526936.5(ENSG00000254777):​n.177-1245G>A 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 0.196 in 152,150 control chromosomes in the GnomAD database, including 3,456 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 0.20 (3454 hom., cov: 31)
  • Exomes 𝑓: 0.15 (2 hom.)
• Consequence: ENST00000526936.5 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0560

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.314 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000526936.5	n.177-1245G>A		intron_variant, non_coding_transcript_variant		5
	ENST00000527672.1	n.324-1245G>A		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.196 AC: 29746 AN: 151882 Hom.: 3441 Cov.: 31

Gnomad AFR AF: 0.319

Gnomad AMI AF: 0.128

Gnomad AMR AF: 0.139

Gnomad ASJ AF: 0.134

Gnomad EAS AF: 0.0602

Gnomad SAS AF: 0.215

Gnomad FIN AF: 0.192

Gnomad MID AF: 0.117

Gnomad NFE AF: 0.149

Gnomad OTH AF: 0.152

GnomAD4 exome AF: 0.153 AC: 23 AN: 150 Hom.: 2 AF XY: 0.140 AC XY: 14 AN XY: 100

Gnomad4 AFR exome AF: 0.250

Gnomad4 AMR exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.150

Gnomad4 NFE exome AF: 0.170

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.196 AC: 29787 AN: 152000 Hom.: 3454 Cov.: 31 AF XY: 0.196 AC XY: 14553 AN XY: 74256

Gnomad4 AFR AF: 0.319

Gnomad4 AMR AF: 0.138

Gnomad4 ASJ AF: 0.134

Gnomad4 EAS AF: 0.0605

Gnomad4 SAS AF: 0.214

Gnomad4 FIN AF: 0.192

Gnomad4 NFE AF: 0.149

Gnomad4 OTH AF: 0.150

Alfa AF: 0.151 Hom.: 2636

Bravo AF: 0.190

Asia WGS AF: 0.148 AC: 513 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	10
DANN	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10104895; hg19: chr8-61876044;