8-88579854-G-T

Position:

• chr8-88579854-G-T

Variant summary

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

The ENST00000665922.1(ENSG00000253553):​n.324+37044G>T 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 0.244 in 151,926 control chromosomes in the GnomAD database, including 5,338 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 0.24 (5338 hom., cov: 31)
• Consequence: ENST00000665922.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.94

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.11).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.392 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105375630	XR_001745653.3	n.355+37044G>T		intron_variant, non_coding_transcript_variant
LOC105375629	XR_928383.4	n.84+8537C>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000665922.1	n.324+37044G>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.243 AC: 36955 AN: 151808 Hom.: 5325 Cov.: 31

Gnomad AFR AF: 0.397

Gnomad AMI AF: 0.302

Gnomad AMR AF: 0.180

Gnomad ASJ AF: 0.195

Gnomad EAS AF: 0.114

Gnomad SAS AF: 0.254

Gnomad FIN AF: 0.144

Gnomad MID AF: 0.237

Gnomad NFE AF: 0.191

Gnomad OTH AF: 0.244

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

GnomAD4 genome AF: 0.244 AC: 36997 AN: 151926 Hom.: 5338 Cov.: 31 AF XY: 0.241 AC XY: 17905 AN XY: 74228

Gnomad4 AFR AF: 0.397

Gnomad4 AMR AF: 0.180

Gnomad4 ASJ AF: 0.195

Gnomad4 EAS AF: 0.115

Gnomad4 SAS AF: 0.253

Gnomad4 FIN AF: 0.144

Gnomad4 NFE AF: 0.191

Gnomad4 OTH AF: 0.244

Alfa AF: 0.255 Hom.: 873

Bravo AF: 0.249

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.30
DANN	Benign	0.094

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11995572; hg19: chr8-89592083;