ENST00000843628.1:n.98-7070G>A

Variant names:

• chr8-9935152-G-A
• rs2055729
• ENST00000843628.1:n.98-7070G>A

Variant summary

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

The ENST00000843628.1(ENSG00000309740):​n.98-7070G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.548 in 151,962 control chromosomes in the GnomAD database, including 24,910 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 0.55 (24910 hom., cov: 31)
• Consequence: ENSG00000309740 ENST00000843628.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.138
• Publications: 17 publications found

Genes affected

ENSG00000309740 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.663 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
ENSG00000309740	ENST00000843628.1	n.98-7070G>A		intron_variant	Intron 1 of 2
ENSG00000309740	ENST00000843629.1	n.174+1053G>A		intron_variant	Intron 1 of 2
ENSG00000309740	ENST00000843630.1	n.170-7070G>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.548 AC: 83243 AN: 151848 Hom.: 24901 Cov.: 31

Gnomad AFR AF: 0.300

Gnomad AMI AF: 0.727

Gnomad AMR AF: 0.637

Gnomad ASJ AF: 0.732

Gnomad EAS AF: 0.390

Gnomad SAS AF: 0.673

Gnomad FIN AF: 0.544

Gnomad MID AF: 0.706

Gnomad NFE AF: 0.668

Gnomad OTH AF: 0.617

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

GnomAD4 genome AF: 0.548 AC: 83255 AN: 151962 Hom.: 24910 Cov.: 31 AF XY: 0.547 AC XY: 40659 AN XY: 74274

African (AFR) AF: 0.299 AC: 12396 AN: 41426

American (AMR) AF: 0.638 AC: 9753 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.732 AC: 2539 AN: 3470

East Asian (EAS) AF: 0.390 AC: 2015 AN: 5168

South Asian (SAS) AF: 0.674 AC: 3241 AN: 4812

European-Finnish (FIN) AF: 0.544 AC: 5732 AN: 10538

Middle Eastern (MID) AF: 0.704 AC: 207 AN: 294

European-Non Finnish (NFE) AF: 0.668 AC: 45423 AN: 67952

Other (OTH) AF: 0.609 AC: 1287 AN: 2112

Alfa AF: 0.624 Hom.: 39602

Bravo AF: 0.539

Asia WGS AF: 0.511 AC: 1776 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.42
DANN	Benign	0.27
PhyloP100		-0.14

Splicing

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

Other links and lift over

dbSNP: rs2055729; hg19: chr8-9792662;