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 ENST00000832857.1(ENSG00000253374):​n.327-37757C>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 ENST00000832857.1 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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000832857.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000253374	ENST00000524085.2	TSL:5	n.299-13967C>G		intron	N/A
	ENSG00000253374	ENST00000832857.1		n.327-37757C>G		intron	N/A
	ENSG00000253374	ENST00000832858.1		n.309-37757C>G		intron	N/A

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 v4.9

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs16909220;

hg19: chr8-82396185;