8-102643566-A-T

Variant names:

• chr8-102643566-A-T
• rs1434278
• ENST00000731667.1:n.163+15577A>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000731667.1(ENSG00000283959):​n.163+15577A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.218 in 152,104 control chromosomes in the GnomAD database, including 4,018 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 0.22 (4018 hom., cov: 32)
• Consequence: ENSG00000283959 ENST00000731667.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.622
• Publications: 2 publications found

Genes affected

ENSG00000283959 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.344 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000283959	ENST00000731667.1	n.163+15577A>T		intron_variant	Intron 1 of 7
ENSG00000283959	ENST00000731685.1	n.229+15577A>T		intron_variant	Intron 1 of 1
ENSG00000283959	ENST00000731692.1	n.358-490A>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.218 AC: 33206 AN: 151986 Hom.: 4008 Cov.: 32

Gnomad AFR AF: 0.152

Gnomad AMI AF: 0.192

Gnomad AMR AF: 0.351

Gnomad ASJ AF: 0.244

Gnomad EAS AF: 0.178

Gnomad SAS AF: 0.192

Gnomad FIN AF: 0.303

Gnomad MID AF: 0.209

Gnomad NFE AF: 0.219

Gnomad OTH AF: 0.235

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

GnomAD4 genome AF: 0.218 AC: 33228 AN: 152104 Hom.: 4018 Cov.: 32 AF XY: 0.225 AC XY: 16718 AN XY: 74342

African (AFR) AF: 0.152 AC: 6323 AN: 41518

American (AMR) AF: 0.352 AC: 5373 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.244 AC: 845 AN: 3468

East Asian (EAS) AF: 0.178 AC: 921 AN: 5178

South Asian (SAS) AF: 0.192 AC: 925 AN: 4814

European-Finnish (FIN) AF: 0.303 AC: 3205 AN: 10564

Middle Eastern (MID) AF: 0.204 AC: 60 AN: 294

European-Non Finnish (NFE) AF: 0.219 AC: 14913 AN: 67994

Other (OTH) AF: 0.232 AC: 489 AN: 2106

Alfa AF: 0.229 Hom.: 544

Bravo AF: 0.222

Asia WGS AF: 0.182 AC: 633 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.58
DANN	Benign	0.59
PhyloP100		-0.62

Splicing

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

Other links and lift over

dbSNP: rs1434278; hg19: chr8-103655794;