chr8-21193724-A-G

Position:

• chr8-21193724-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+101410T>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 0.444 in 152,032 control chromosomes in the GnomAD database, including 19,367 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 0.44 (19367 hom., cov: 32)
• Consequence: ENST00000659453.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.40

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.811 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+101410T>C		intron_variant, non_coding_transcript_variant
	ENST00000657734.1	n.1326+101410T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.444 AC: 67411 AN: 151914 Hom.: 19317 Cov.: 32

Gnomad AFR AF: 0.818

Gnomad AMI AF: 0.231

Gnomad AMR AF: 0.349

Gnomad ASJ AF: 0.378

Gnomad EAS AF: 0.256

Gnomad SAS AF: 0.471

Gnomad FIN AF: 0.224

Gnomad MID AF: 0.443

Gnomad NFE AF: 0.290

Gnomad OTH AF: 0.432

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

GnomAD4 genome AF: 0.444 AC: 67511 AN: 152032 Hom.: 19367 Cov.: 32 AF XY: 0.440 AC XY: 32699 AN XY: 74336

Gnomad4 AFR AF: 0.819

Gnomad4 AMR AF: 0.349

Gnomad4 ASJ AF: 0.378

Gnomad4 EAS AF: 0.256

Gnomad4 SAS AF: 0.473

Gnomad4 FIN AF: 0.224

Gnomad4 NFE AF: 0.290

Gnomad4 OTH AF: 0.428

Alfa AF: 0.324 Hom.: 18156

Bravo AF: 0.470

Asia WGS AF: 0.407 AC: 1418 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.091
DANN	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2613675; hg19: chr8-21051235;