chr6-15803001-A-C

Variant names:

• chr6-15803001-A-C
• rs387816
• ENST00000806821.1:n.317+11997A>C

Variant summary

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

The ENST00000806821.1(ENSG00000289953):​n.317+11997A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.554 in 151,926 control chromosomes in the GnomAD database, including 23,716 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 0.55 (23716 hom., cov: 31)
• Consequence: ENSG00000289953 ENST00000806821.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.181
• Publications: 3 publications found

Genes affected

ENSG00000289953 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.588 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
ENSG00000289953	ENST00000806821.1	n.317+11997A>C		intron_variant	Intron 1 of 3
ENSG00000289953	ENST00000806822.1	n.331+11997A>C		intron_variant	Intron 1 of 3
ENSG00000289953	ENST00000806826.1	n.331+11997A>C		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.554 AC: 84172 AN: 151808 Hom.: 23692 Cov.: 31

Gnomad AFR AF: 0.544

Gnomad AMI AF: 0.571

Gnomad AMR AF: 0.529

Gnomad ASJ AF: 0.603

Gnomad EAS AF: 0.242

Gnomad SAS AF: 0.436

Gnomad FIN AF: 0.579

Gnomad MID AF: 0.506

Gnomad NFE AF: 0.593

Gnomad OTH AF: 0.545

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

GnomAD4 genome AF: 0.554 AC: 84237 AN: 151926 Hom.: 23716 Cov.: 31 AF XY: 0.549 AC XY: 40748 AN XY: 74228

African (AFR) AF: 0.544 AC: 22527 AN: 41416

American (AMR) AF: 0.529 AC: 8078 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.603 AC: 2093 AN: 3472

East Asian (EAS) AF: 0.242 AC: 1253 AN: 5168

South Asian (SAS) AF: 0.437 AC: 2102 AN: 4806

European-Finnish (FIN) AF: 0.579 AC: 6089 AN: 10524

Middle Eastern (MID) AF: 0.497 AC: 146 AN: 294

European-Non Finnish (NFE) AF: 0.593 AC: 40288 AN: 67952

Other (OTH) AF: 0.539 AC: 1141 AN: 2116

Alfa AF: 0.576 Hom.: 105250

Bravo AF: 0.547

Asia WGS AF: 0.351 AC: 1220 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.8
DANN	Benign	0.44
PhyloP100		0.18

Splicing

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

Other links and lift over

dbSNP: rs387816; hg19: chr6-15803232;