8-33907608-A-C

Position:

• chr8-33907608-A-C

Variant summary

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

The ENST00000523063.5(ENSG00000253642):​n.505-100248A>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 0.449 in 151,890 control chromosomes in the GnomAD database, including 15,808 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 0.45 (15808 hom., cov: 32)
• Consequence: ENST00000523063.5 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.639

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.775 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105379364	XR_002956701.2	n.288-100248A>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000523063.5	n.505-100248A>C		intron_variant, non_coding_transcript_variant		3
	ENST00000523336.2	n.148-100248A>C		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.449 AC: 68142 AN: 151772 Hom.: 15791 Cov.: 32

Gnomad AFR AF: 0.410

Gnomad AMI AF: 0.364

Gnomad AMR AF: 0.429

Gnomad ASJ AF: 0.324

Gnomad EAS AF: 0.795

Gnomad SAS AF: 0.624

Gnomad FIN AF: 0.417

Gnomad MID AF: 0.338

Gnomad NFE AF: 0.452

Gnomad OTH AF: 0.434

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

GnomAD4 genome AF: 0.449 AC: 68185 AN: 151890 Hom.: 15808 Cov.: 32 AF XY: 0.449 AC XY: 33348 AN XY: 74210

Gnomad4 AFR AF: 0.410

Gnomad4 AMR AF: 0.430

Gnomad4 ASJ AF: 0.324

Gnomad4 EAS AF: 0.795

Gnomad4 SAS AF: 0.624

Gnomad4 FIN AF: 0.417

Gnomad4 NFE AF: 0.452

Gnomad4 OTH AF: 0.437

Alfa AF: 0.452 Hom.: 32499

Bravo AF: 0.446

Asia WGS AF: 0.680 AC: 2362 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	4.4
DANN	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11776207; hg19: chr8-33765126;