rs6469101

Variant names:

• chr8-107240010-G-A
• rs6469101
• ENST00000801168.1:n.196+593C>T

Variant summary

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

The ENST00000801168.1(ENSG00000304228):​n.196+593C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.19 in 152,098 control chromosomes in the GnomAD database, including 2,894 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 0.19 (2894 hom., cov: 32)
• Consequence: ENSG00000304228 ENST00000801168.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.37
• Publications: 6 publications found

Genes affected

ENSG00000304228 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.301 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
ENSG00000304228	ENST00000801168.1	n.196+593C>T		intron_variant	Intron 2 of 2
ENSG00000304228	ENST00000801169.1	n.383+593C>T		intron_variant	Intron 1 of 1
ENSG00000304228	ENST00000801170.1	n.175+593C>T		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.190 AC: 28872 AN: 151980 Hom.: 2896 Cov.: 32

Gnomad AFR AF: 0.195

Gnomad AMI AF: 0.151

Gnomad AMR AF: 0.224

Gnomad ASJ AF: 0.115

Gnomad EAS AF: 0.314

Gnomad SAS AF: 0.168

Gnomad FIN AF: 0.237

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.169

Gnomad OTH AF: 0.186

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

GnomAD4 genome AF: 0.190 AC: 28877 AN: 152098 Hom.: 2894 Cov.: 32 AF XY: 0.195 AC XY: 14512 AN XY: 74316

African (AFR) AF: 0.194 AC: 8065 AN: 41506

American (AMR) AF: 0.223 AC: 3412 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.115 AC: 398 AN: 3468

East Asian (EAS) AF: 0.314 AC: 1624 AN: 5170

South Asian (SAS) AF: 0.168 AC: 809 AN: 4818

European-Finnish (FIN) AF: 0.237 AC: 2503 AN: 10542

Middle Eastern (MID) AF: 0.0782 AC: 23 AN: 294

European-Non Finnish (NFE) AF: 0.169 AC: 11514 AN: 67998

Other (OTH) AF: 0.186 AC: 391 AN: 2106

Alfa AF: 0.172 Hom.: 9972

Bravo AF: 0.189

Asia WGS AF: 0.256 AC: 890 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	3.4
DANN	Benign	0.24
PhyloP100		1.4

Splicing

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

Other links and lift over

dbSNP: rs6469101; hg19: chr8-108252238;