chr8-11480874-A-G

Variant names:

• chr8-11480874-A-G
• rs62489069
• ENST00000644741.1:n.64+131T>C

Variant summary

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

The ENST00000644741.1(ENSG00000284957):​n.64+131T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.302 in 151,874 control chromosomes in the GnomAD database, including 7,962 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 0.30 (7958 hom., cov: 31)
  • Exomes 𝑓: 0.33 (4 hom.)
• Consequence: ENSG00000284957 ENST00000644741.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.114
• Publications: 11 publications found

Genes affected

ENSG00000284957 (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 (EAS) allele frequency at 95% confidence interval = 0.72 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000284957	ENST00000644741.1	n.64+131T>C		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.302 AC: 45877 AN: 151676 Hom.: 7940 Cov.: 31

Gnomad AFR AF: 0.221

Gnomad AMI AF: 0.311

Gnomad AMR AF: 0.462

Gnomad ASJ AF: 0.208

Gnomad EAS AF: 0.740

Gnomad SAS AF: 0.413

Gnomad FIN AF: 0.297

Gnomad MID AF: 0.255

Gnomad NFE AF: 0.281

Gnomad OTH AF: 0.302

GnomAD4 exome AF: 0.325 AC: 26 AN: 80 Hom.: 4 AF XY: 0.338 AC XY: 23 AN XY: 68

African (AFR) AC: 0 AN: 0

American (AMR) AF: 0.00 AC: 0 AN: 2

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AF: 0.00 AC: 0 AN: 2

European-Finnish (FIN) AF: 0.500 AC: 2 AN: 4

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.324 AC: 22 AN: 68

Other (OTH) AF: 0.500 AC: 2 AN: 4

GnomAD4 genome AF: 0.302 AC: 45912 AN: 151794 Hom.: 7958 Cov.: 31 AF XY: 0.310 AC XY: 22963 AN XY: 74170

African (AFR) AF: 0.220 AC: 9124 AN: 41396

American (AMR) AF: 0.463 AC: 7055 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.208 AC: 722 AN: 3472

East Asian (EAS) AF: 0.740 AC: 3803 AN: 5140

South Asian (SAS) AF: 0.411 AC: 1972 AN: 4798

European-Finnish (FIN) AF: 0.297 AC: 3131 AN: 10540

Middle Eastern (MID) AF: 0.257 AC: 75 AN: 292

European-Non Finnish (NFE) AF: 0.281 AC: 19094 AN: 67900

Other (OTH) AF: 0.311 AC: 654 AN: 2102

Alfa AF: 0.265 Hom.: 701

Bravo AF: 0.318

Asia WGS AF: 0.585 AC: 2030 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.0
DANN	Benign	0.53
PhyloP100		-0.11

Splicing

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

Other links and lift over

dbSNP: rs62489069; hg19: chr8-11338383;