chr8-109051931-G-T

Variant names:

• chr8-109051931-G-T
• rs4276659
• ENST00000522244.1:n.130-7804C>A

Variant summary

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

The ENST00000522244.1(ENSG00000253796):​n.130-7804C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.637 in 152,080 control chromosomes in the GnomAD database, including 31,744 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 0.64 (31744 hom., cov: 32)
• Consequence: ENSG00000253796 ENST00000522244.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.329
• Publications: 2 publications found

Genes affected

ENSG00000253796 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.762 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000522244.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000253796	ENST00000522244.1	TSL:3	n.130-7804C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.637 AC: 96858 AN: 151962 Hom.: 31708 Cov.: 32

Gnomad AFR AF: 0.769

Gnomad AMI AF: 0.729

Gnomad AMR AF: 0.718

Gnomad ASJ AF: 0.519

Gnomad EAS AF: 0.714

Gnomad SAS AF: 0.606

Gnomad FIN AF: 0.535

Gnomad MID AF: 0.415

Gnomad NFE AF: 0.558

Gnomad OTH AF: 0.620

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

GnomAD4 genome AF: 0.637 AC: 96949 AN: 152080 Hom.: 31744 Cov.: 32 AF XY: 0.639 AC XY: 47473 AN XY: 74326

African (AFR) AF: 0.769 AC: 31876 AN: 41474

American (AMR) AF: 0.718 AC: 10980 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.519 AC: 1800 AN: 3468

East Asian (EAS) AF: 0.715 AC: 3685 AN: 5154

South Asian (SAS) AF: 0.605 AC: 2917 AN: 4822

European-Finnish (FIN) AF: 0.535 AC: 5656 AN: 10570

Middle Eastern (MID) AF: 0.408 AC: 120 AN: 294

European-Non Finnish (NFE) AF: 0.558 AC: 37948 AN: 67988

Other (OTH) AF: 0.618 AC: 1305 AN: 2112

Alfa AF: 0.550 Hom.: 3228

Bravo AF: 0.660

Asia WGS AF: 0.675 AC: 2346 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.3
DANN	Benign	0.30
PhyloP100		0.33

Splicing

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

Other links and lift over

dbSNP: rs4276659; hg19: chr8-110064160;