8-81483950-C-G

Variant names:

• chr8-81483950-C-G
• rs16909220
• ENST00000524085.2:n.299-13967C>G

Variant summary

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

The ENST00000524085.2(ENSG00000253374):​n.299-13967C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.156 in 152,172 control chromosomes in the GnomAD database, including 1,920 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 0.16 (1920 hom., cov: 32)
• Consequence: ENSG00000253374 ENST00000524085.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0300
• Publications: 2 publications found

Genes affected

ENSG00000253374 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.165 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC101927118	XR_001745980.2	n.517+21976C>G		intron_variant	Intron 1 of 8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000253374	ENST00000524085.2	n.299-13967C>G		intron_variant	Intron 2 of 3	5
ENSG00000253374	ENST00000832857.1	n.327-37757C>G		intron_variant	Intron 2 of 9
ENSG00000253374	ENST00000832858.1	n.309-37757C>G		intron_variant	Intron 2 of 9
ENSG00000253374	ENST00000832859.1	n.328-37757C>G		intron_variant	Intron 2 of 5

Frequencies

GnomAD3 genomes AF: 0.156 AC: 23748 AN: 152054 Hom.: 1914 Cov.: 32

Gnomad AFR AF: 0.163

Gnomad AMI AF: 0.0855

Gnomad AMR AF: 0.143

Gnomad ASJ AF: 0.171

Gnomad EAS AF: 0.0678

Gnomad SAS AF: 0.170

Gnomad FIN AF: 0.116

Gnomad MID AF: 0.182

Gnomad NFE AF: 0.167

Gnomad OTH AF: 0.151

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

GnomAD4 genome AF: 0.156 AC: 23787 AN: 152172 Hom.: 1920 Cov.: 32 AF XY: 0.154 AC XY: 11431 AN XY: 74384

African (AFR) AF: 0.163 AC: 6752 AN: 41506

American (AMR) AF: 0.143 AC: 2193 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.171 AC: 592 AN: 3468

East Asian (EAS) AF: 0.0680 AC: 352 AN: 5180

South Asian (SAS) AF: 0.172 AC: 830 AN: 4820

European-Finnish (FIN) AF: 0.116 AC: 1232 AN: 10598

Middle Eastern (MID) AF: 0.178 AC: 52 AN: 292

European-Non Finnish (NFE) AF: 0.167 AC: 11381 AN: 67992

Other (OTH) AF: 0.154 AC: 325 AN: 2116

Alfa AF: 0.168 Hom.: 265

Bravo AF: 0.156

Asia WGS AF: 0.124 AC: 430 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	0.94
DANN	Benign	0.59
PhyloP100		-0.030

Splicing

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

Other links and lift over

dbSNP: rs16909220; hg19: chr8-82396185;