chr8-21230272-A-G

Position:

• chr8-21230272-A-G

Variant summary

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

The ENST00000659453.1(ENSG00000254092):​n.1639+64862T>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 0.416 in 151,912 control chromosomes in the GnomAD database, including 17,178 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 0.42 (17178 hom., cov: 31)
• Consequence: ENST00000659453.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.293

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.767 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
	ENST00000659453.1	n.1639+64862T>C		intron_variant, non_coding_transcript_variant
	ENST00000657734.1	n.1326+64862T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.416 AC: 63157 AN: 151794 Hom.: 17130 Cov.: 31

Gnomad AFR AF: 0.774

Gnomad AMI AF: 0.291

Gnomad AMR AF: 0.311

Gnomad ASJ AF: 0.373

Gnomad EAS AF: 0.176

Gnomad SAS AF: 0.433

Gnomad FIN AF: 0.203

Gnomad MID AF: 0.421

Gnomad NFE AF: 0.276

Gnomad OTH AF: 0.415

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

GnomAD4 genome AF: 0.416 AC: 63248 AN: 151912 Hom.: 17178 Cov.: 31 AF XY: 0.409 AC XY: 30402 AN XY: 74264

Gnomad4 AFR AF: 0.774

Gnomad4 AMR AF: 0.310

Gnomad4 ASJ AF: 0.373

Gnomad4 EAS AF: 0.175

Gnomad4 SAS AF: 0.434

Gnomad4 FIN AF: 0.203

Gnomad4 NFE AF: 0.276

Gnomad4 OTH AF: 0.411

Alfa AF: 0.303 Hom.: 15434

Bravo AF: 0.441

Asia WGS AF: 0.371 AC: 1290 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.53
DANN	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs989329; hg19: chr8-21087783;