rs6474491

Variant names:

• chr8-38156330-T-C
• rs6474491
• ENST00000520598.1:n.100-6980T>C

Your query was ambiguous. Multiple possible variants found:

• chr8-38156330-T-C
• chr8-38156330-T-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000520598.1(ENSG00000253356):​n.100-6980T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.246 in 152,010 control chromosomes in the GnomAD database, including 4,759 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 0.25 (4759 hom., cov: 31)
• Consequence: ENSG00000253356 ENST00000520598.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.164

Genes affected

ENSG00000253356 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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 = 0.368 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105379382	XR_949687.2	n.-9T>C		upstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000253356	ENST00000520598.1	n.100-6980T>C		intron_variant	Intron 1 of 1	4

Frequencies

GnomAD3 genomes AF: 0.246 AC: 37395 AN: 151890 Hom.: 4761 Cov.: 31

Gnomad AFR AF: 0.233

Gnomad AMI AF: 0.324

Gnomad AMR AF: 0.218

Gnomad ASJ AF: 0.270

Gnomad EAS AF: 0.332

Gnomad SAS AF: 0.382

Gnomad FIN AF: 0.208

Gnomad MID AF: 0.335

Gnomad NFE AF: 0.247

Gnomad OTH AF: 0.253

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

GnomAD4 genome AF: 0.246 AC: 37419 AN: 152010 Hom.: 4759 Cov.: 31 AF XY: 0.247 AC XY: 18362 AN XY: 74286

Gnomad4 AFR AF: 0.233

Gnomad4 AMR AF: 0.218

Gnomad4 ASJ AF: 0.270

Gnomad4 EAS AF: 0.332

Gnomad4 SAS AF: 0.382

Gnomad4 FIN AF: 0.208

Gnomad4 NFE AF: 0.247

Gnomad4 OTH AF: 0.256

Alfa AF: 0.253 Hom.: 6616

Bravo AF: 0.243

Asia WGS AF: 0.344 AC: 1197 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	3.6
DANN	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6474491; hg19: chr8-38013848;