chr6-65888301-G-A

Variant names:

• chr6-65888301-G-A
• rs10455590
• ENST00000800215.1:n.218+12652C>T

Variant summary

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

The ENST00000800215.1(ENSG00000304165):​n.218+12652C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.337 in 152,000 control chromosomes in the GnomAD database, including 9,956 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 0.34 (9956 hom., cov: 32)
• Consequence: ENSG00000304165 ENST00000800215.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.190
• Publications: 7 publications found

Genes affected

ENSG00000304165 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.447 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
ENSG00000304165	ENST00000800215.1	n.218+12652C>T		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.338 AC: 51285 AN: 151880 Hom.: 9957 Cov.: 32

Gnomad AFR AF: 0.155

Gnomad AMI AF: 0.491

Gnomad AMR AF: 0.305

Gnomad ASJ AF: 0.484

Gnomad EAS AF: 0.152

Gnomad SAS AF: 0.295

Gnomad FIN AF: 0.409

Gnomad MID AF: 0.446

Gnomad NFE AF: 0.451

Gnomad OTH AF: 0.372

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

GnomAD4 genome AF: 0.337 AC: 51290 AN: 152000 Hom.: 9956 Cov.: 32 AF XY: 0.332 AC XY: 24626 AN XY: 74272

African (AFR) AF: 0.155 AC: 6414 AN: 41496

American (AMR) AF: 0.304 AC: 4631 AN: 15226

Ashkenazi Jewish (ASJ) AF: 0.484 AC: 1681 AN: 3472

East Asian (EAS) AF: 0.152 AC: 785 AN: 5158

South Asian (SAS) AF: 0.296 AC: 1429 AN: 4822

European-Finnish (FIN) AF: 0.409 AC: 4313 AN: 10556

Middle Eastern (MID) AF: 0.456 AC: 134 AN: 294

European-Non Finnish (NFE) AF: 0.451 AC: 30678 AN: 67956

Other (OTH) AF: 0.369 AC: 780 AN: 2114

Alfa AF: 0.432 Hom.: 23344

Bravo AF: 0.322

Asia WGS AF: 0.224 AC: 782 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.6
DANN	Benign	0.70
PhyloP100		0.19

Splicing

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

Other links and lift over

dbSNP: rs10455590; hg19: chr6-66598194;