8-16851103-T-G

Variant names:

• chr8-16851103-T-G
• rs1697633
• ENST00000521411.2:n.128-6848A>C

Variant summary

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

The ENST00000521411.2(ENSG00000253496):​n.128-6848A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.824 in 152,042 control chromosomes in the GnomAD database, including 52,463 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 0.82 (52463 hom., cov: 32)
• Consequence: ENSG00000253496 ENST00000521411.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.145
• Publications: 1 publications found

Genes affected

ENSG00000253496 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.898 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105379297	XR_949525.1	n.157+63815A>C		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000253496	ENST00000521411.2	n.128-6848A>C		intron_variant	Intron 1 of 3	5
ENSG00000253496	ENST00000755781.1	n.228+63815A>C		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.824 AC: 125189 AN: 151924 Hom.: 52444 Cov.: 32

Gnomad AFR AF: 0.730

Gnomad AMI AF: 0.905

Gnomad AMR AF: 0.793

Gnomad ASJ AF: 0.891

Gnomad EAS AF: 0.455

Gnomad SAS AF: 0.792

Gnomad FIN AF: 0.882

Gnomad MID AF: 0.896

Gnomad NFE AF: 0.904

Gnomad OTH AF: 0.840

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

GnomAD4 genome AF: 0.824 AC: 125255 AN: 152042 Hom.: 52463 Cov.: 32 AF XY: 0.820 AC XY: 60966 AN XY: 74322

African (AFR) AF: 0.730 AC: 30250 AN: 41418

American (AMR) AF: 0.792 AC: 12102 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.891 AC: 3092 AN: 3470

East Asian (EAS) AF: 0.454 AC: 2345 AN: 5166

South Asian (SAS) AF: 0.792 AC: 3819 AN: 4824

European-Finnish (FIN) AF: 0.882 AC: 9320 AN: 10566

Middle Eastern (MID) AF: 0.891 AC: 262 AN: 294

European-Non Finnish (NFE) AF: 0.904 AC: 61470 AN: 68008

Other (OTH) AF: 0.838 AC: 1770 AN: 2112

Alfa AF: 0.840 Hom.: 3055

Bravo AF: 0.812

Asia WGS AF: 0.632 AC: 2199 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	8.9
DANN	Benign	0.87
PhyloP100		-0.14

Splicing

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

Other links and lift over

dbSNP: rs1697633; hg19: chr8-16708612;