chr5-100006343-A-G

Variant names:

• chr5-100006343-A-G
• rs10067427
• ENST00000772664.1:n.462+28118T>C

Variant summary

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

The ENST00000772664.1(ENSG00000300549):​n.462+28118T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.422 in 148,852 control chromosomes in the GnomAD database, including 15,132 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 0.42 (15132 hom., cov: 25)
• Consequence: ENSG00000300549 ENST00000772664.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.499
• Publications: 12 publications found

Genes affected

ENSG00000300549 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.656 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
ENSG00000300549	ENST00000772664.1	n.462+28118T>C		intron_variant	Intron 4 of 4

Frequencies

GnomAD3 genomes AF: 0.422 AC: 62801 AN: 148752 Hom.: 15092 Cov.: 25

Gnomad AFR AF: 0.662

Gnomad AMI AF: 0.252

Gnomad AMR AF: 0.348

Gnomad ASJ AF: 0.406

Gnomad EAS AF: 0.264

Gnomad SAS AF: 0.198

Gnomad FIN AF: 0.301

Gnomad MID AF: 0.424

Gnomad NFE AF: 0.345

Gnomad OTH AF: 0.439

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

GnomAD4 genome AF: 0.422 AC: 62881 AN: 148852 Hom.: 15132 Cov.: 25 AF XY: 0.415 AC XY: 30064 AN XY: 72452

African (AFR) AF: 0.662 AC: 26548 AN: 40076

American (AMR) AF: 0.348 AC: 5182 AN: 14912

Ashkenazi Jewish (ASJ) AF: 0.406 AC: 1403 AN: 3458

East Asian (EAS) AF: 0.264 AC: 1345 AN: 5100

South Asian (SAS) AF: 0.199 AC: 940 AN: 4730

European-Finnish (FIN) AF: 0.301 AC: 2944 AN: 9786

Middle Eastern (MID) AF: 0.432 AC: 126 AN: 292

European-Non Finnish (NFE) AF: 0.345 AC: 23265 AN: 67522

Other (OTH) AF: 0.435 AC: 899 AN: 2068

Alfa AF: 0.380 Hom.: 35271

Bravo AF: 0.446

Asia WGS AF: 0.248 AC: 864 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.93
DANN	Benign	0.83
PhyloP100		-0.50

Splicing

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

Other links and lift over

dbSNP: rs10067427; hg19: chr5-99342047;