chr6-16108932-A-C

Variant names:

• chr6-16108932-A-C
• rs2294261
• ENST00000806821.1:n.590-12482A>C

Variant summary

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

The ENST00000806821.1(ENSG00000289953):​n.590-12482A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.648 in 152,078 control chromosomes in the GnomAD database, including 34,279 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 0.65 (34279 hom., cov: 32)
• Consequence: ENSG00000289953 ENST00000806821.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.468
• Publications: 9 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=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.886 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.590-12482A>C		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.648 AC: 98482 AN: 151960 Hom.: 34219 Cov.: 32

Gnomad AFR AF: 0.894

Gnomad AMI AF: 0.458

Gnomad AMR AF: 0.640

Gnomad ASJ AF: 0.592

Gnomad EAS AF: 0.902

Gnomad SAS AF: 0.659

Gnomad FIN AF: 0.473

Gnomad MID AF: 0.528

Gnomad NFE AF: 0.515

Gnomad OTH AF: 0.602

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

GnomAD4 genome AF: 0.648 AC: 98597 AN: 152078 Hom.: 34279 Cov.: 32 AF XY: 0.647 AC XY: 48069 AN XY: 74338

African (AFR) AF: 0.894 AC: 37098 AN: 41506

American (AMR) AF: 0.641 AC: 9788 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.592 AC: 2051 AN: 3466

East Asian (EAS) AF: 0.902 AC: 4673 AN: 5180

South Asian (SAS) AF: 0.658 AC: 3170 AN: 4820

European-Finnish (FIN) AF: 0.473 AC: 4994 AN: 10556

Middle Eastern (MID) AF: 0.527 AC: 155 AN: 294

European-Non Finnish (NFE) AF: 0.515 AC: 34973 AN: 67956

Other (OTH) AF: 0.606 AC: 1279 AN: 2112

Alfa AF: 0.556 Hom.: 40868

Bravo AF: 0.673

Asia WGS AF: 0.818 AC: 2844 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	3.4
DANN	Benign	0.78
PhyloP100		-0.47

Splicing

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

Other links and lift over

dbSNP: rs2294261; hg19: chr6-16109163;