chr8-11480874-A-G

Position:

• chr8-11480874-A-G

Variant summary

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

The ENST00000644741.1(ENSG00000284957):​n.64+131T>C 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 0.302 in 151,874 control chromosomes in the GnomAD database, including 7,962 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 0.30 (7958 hom., cov: 31)
  • Exomes 𝑓: 0.33 (4 hom.)
• Consequence: ENST00000644741.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.114

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 (EAS) allele frequency at 95% confidence interval = 0.72 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000644741.1	n.64+131T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.302 AC: 45877 AN: 151676 Hom.: 7940 Cov.: 31

Gnomad AFR AF: 0.221

Gnomad AMI AF: 0.311

Gnomad AMR AF: 0.462

Gnomad ASJ AF: 0.208

Gnomad EAS AF: 0.740

Gnomad SAS AF: 0.413

Gnomad FIN AF: 0.297

Gnomad MID AF: 0.255

Gnomad NFE AF: 0.281

Gnomad OTH AF: 0.302

GnomAD4 exome AF: 0.325 AC: 26 AN: 80 Hom.: 4 AF XY: 0.338 AC XY: 23 AN XY: 68

Gnomad4 AMR exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.500

Gnomad4 NFE exome AF: 0.324

Gnomad4 OTH exome AF: 0.500

GnomAD4 genome AF: 0.302 AC: 45912 AN: 151794 Hom.: 7958 Cov.: 31 AF XY: 0.310 AC XY: 22963 AN XY: 74170

Gnomad4 AFR AF: 0.220

Gnomad4 AMR AF: 0.463

Gnomad4 ASJ AF: 0.208

Gnomad4 EAS AF: 0.740

Gnomad4 SAS AF: 0.411

Gnomad4 FIN AF: 0.297

Gnomad4 NFE AF: 0.281

Gnomad4 OTH AF: 0.311

Alfa AF: 0.265 Hom.: 701

Bravo AF: 0.318

Asia WGS AF: 0.585 AC: 2030 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.0
DANN	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs62489069; hg19: chr8-11338383;