8-8643812-T-G

Variant summary

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

The ENST00000690140.1(ENSG00000289622):n.309-10974T>G 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 0.261 in 151,994 control chromosomes in the GnomAD database, including 5,377 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 0.26 (5377 hom., cov: 31)
• Consequence: ENST00000690140.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00400

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.324 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
	ENST00000690140.1	n.309-10974T>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.261 AC: 39669 AN: 151876 Hom.: 5374 Cov.: 31

Gnomad AFR AF: 0.282

Gnomad AMI AF: 0.227

Gnomad AMR AF: 0.172

Gnomad ASJ AF: 0.211

Gnomad EAS AF: 0.336

Gnomad SAS AF: 0.254

Gnomad FIN AF: 0.352

Gnomad MID AF: 0.193

Gnomad NFE AF: 0.253

Gnomad OTH AF: 0.228

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

GnomAD4 genome AF: 0.261 AC: 39705 AN: 151994 Hom.: 5377 Cov.: 31 AF XY: 0.265 AC XY: 19698 AN XY: 74282

Gnomad4 AFR AF: 0.282

Gnomad4 AMR AF: 0.172

Gnomad4 ASJ AF: 0.211

Gnomad4 EAS AF: 0.337

Gnomad4 SAS AF: 0.255

Gnomad4 FIN AF: 0.352

Gnomad4 NFE AF: 0.253

Gnomad4 OTH AF: 0.226

Alfa AF: 0.243 Hom.: 7635

Bravo AF: 0.252

Asia WGS AF: 0.253 AC: 880 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
Cadd	Benign	3.0
Dann	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7013418; hg19: chr8-8501322;