chr8-95174427-T-C

Variant names:

• chr8-95174427-T-C
• rs297573
• ENST00000812778.1:n.401+939A>G

Variant summary

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

The ENST00000812778.1(ENSG00000305752):​n.401+939A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.319 in 151,864 control chromosomes in the GnomAD database, including 7,915 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 0.32 (7915 hom., cov: 30)
• Consequence: ENSG00000305752 ENST00000812778.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.58
• Publications: 1 publications found

Genes affected

ENSG00000305752 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (AFR) 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
LOC124901982	XR_007061015.1	n.1835-7585T>C		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000305752	ENST00000812778.1	n.401+939A>G		intron_variant	Intron 2 of 2
ENSG00000305765	ENST00000812840.1	n.177-627T>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.319 AC: 48360 AN: 151746 Hom.: 7905 Cov.: 30

Gnomad AFR AF: 0.349

Gnomad AMI AF: 0.277

Gnomad AMR AF: 0.239

Gnomad ASJ AF: 0.313

Gnomad EAS AF: 0.269

Gnomad SAS AF: 0.192

Gnomad FIN AF: 0.272

Gnomad MID AF: 0.331

Gnomad NFE AF: 0.338

Gnomad OTH AF: 0.329

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

GnomAD4 genome AF: 0.319 AC: 48398 AN: 151864 Hom.: 7915 Cov.: 30 AF XY: 0.312 AC XY: 23130 AN XY: 74220

African (AFR) AF: 0.349 AC: 14444 AN: 41366

American (AMR) AF: 0.239 AC: 3651 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.313 AC: 1087 AN: 3470

East Asian (EAS) AF: 0.269 AC: 1396 AN: 5180

South Asian (SAS) AF: 0.191 AC: 919 AN: 4802

European-Finnish (FIN) AF: 0.272 AC: 2865 AN: 10540

Middle Eastern (MID) AF: 0.346 AC: 101 AN: 292

European-Non Finnish (NFE) AF: 0.339 AC: 22998 AN: 67936

Other (OTH) AF: 0.326 AC: 685 AN: 2102

Alfa AF: 0.333 Hom.: 35900

Bravo AF: 0.320

Asia WGS AF: 0.247 AC: 859 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	14
DANN	Benign	0.82
PhyloP100		1.6

Splicing

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

Other links and lift over

dbSNP: rs297573; hg19: chr8-96186655;