rs2067807

Variant names:

• chr8-83952610-T-C
• rs2067807
• ENST00000523678.1:n.123+39775T>C

Variant summary

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

The ENST00000523678.1(ENSG00000254202):​n.123+39775T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0639 in 152,026 control chromosomes in the GnomAD database, including 407 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 0.064 (407 hom., cov: 32)
• Consequence: ENSG00000254202 ENST00000523678.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.791
• Publications: 3 publications found

Genes affected

ENSG00000254202 (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 (SAS) allele frequency at 95% confidence interval = 0.157 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124901968	XR_007060983.1	n.141-14718T>C		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000254202	ENST00000523678.1	n.123+39775T>C		intron_variant	Intron 1 of 3	3
ENSG00000254202	ENST00000752019.1	n.142-1713T>C		intron_variant	Intron 1 of 2
ENSG00000254202	ENST00000752020.1	n.142-11470T>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.0638 AC: 9696 AN: 151906 Hom.: 406 Cov.: 32

Gnomad AFR AF: 0.0379

Gnomad AMI AF: 0.0208

Gnomad AMR AF: 0.0567

Gnomad ASJ AF: 0.0329

Gnomad EAS AF: 0.148

Gnomad SAS AF: 0.166

Gnomad FIN AF: 0.0560

Gnomad MID AF: 0.0348

Gnomad NFE AF: 0.0710

Gnomad OTH AF: 0.0679

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

GnomAD4 genome AF: 0.0639 AC: 9708 AN: 152026 Hom.: 407 Cov.: 32 AF XY: 0.0657 AC XY: 4883 AN XY: 74326

African (AFR) AF: 0.0379 AC: 1575 AN: 41528

American (AMR) AF: 0.0566 AC: 862 AN: 15218

Ashkenazi Jewish (ASJ) AF: 0.0329 AC: 114 AN: 3464

East Asian (EAS) AF: 0.148 AC: 766 AN: 5170

South Asian (SAS) AF: 0.167 AC: 803 AN: 4820

European-Finnish (FIN) AF: 0.0560 AC: 595 AN: 10616

Middle Eastern (MID) AF: 0.0374 AC: 11 AN: 294

European-Non Finnish (NFE) AF: 0.0710 AC: 4818 AN: 67892

Other (OTH) AF: 0.0687 AC: 145 AN: 2112

Alfa AF: 0.0731 Hom.: 292

Bravo AF: 0.0611

Asia WGS AF: 0.174 AC: 607 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.50
DANN	Benign	0.68
PhyloP100		-0.79

Splicing

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

Other links and lift over

dbSNP: rs2067807; hg19: chr8-84864845;