6-52966063-T-C

Variant names:

• chr6-52966063-T-C
• rs560788
• ENST00000448991.7:n.85+7044A>G

Variant summary

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

The ENST00000448991.7(ENSG00000291036):​n.85+7044A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.505 in 152,022 control chromosomes in the GnomAD database, including 20,022 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 0.51 (20022 hom., cov: 31)
• Consequence: ENSG00000291036 ENST00000448991.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.89
• Publications: 6 publications found

Genes affected

ENSG00000291036 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.735 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
ENSG00000291036	ENST00000448991.7	n.85+7044A>G		intron_variant	Intron 1 of 5	3
ENSG00000291036	ENST00000763228.1	n.48+7044A>G		intron_variant	Intron 1 of 4
ENSG00000291036	ENST00000763229.1	n.29+7044A>G		intron_variant	Intron 1 of 3
ENSG00000291036	ENST00000763230.1	n.29+7044A>G		intron_variant	Intron 1 of 4

Frequencies

GnomAD3 genomes AF: 0.505 AC: 76756 AN: 151904 Hom.: 20019 Cov.: 31

Gnomad AFR AF: 0.381

Gnomad AMI AF: 0.496

Gnomad AMR AF: 0.466

Gnomad ASJ AF: 0.500

Gnomad EAS AF: 0.755

Gnomad SAS AF: 0.592

Gnomad FIN AF: 0.555

Gnomad MID AF: 0.560

Gnomad NFE AF: 0.557

Gnomad OTH AF: 0.509

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

GnomAD4 genome AF: 0.505 AC: 76779 AN: 152022 Hom.: 20022 Cov.: 31 AF XY: 0.507 AC XY: 37668 AN XY: 74296

African (AFR) AF: 0.381 AC: 15774 AN: 41454

American (AMR) AF: 0.466 AC: 7116 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.500 AC: 1732 AN: 3464

East Asian (EAS) AF: 0.754 AC: 3896 AN: 5164

South Asian (SAS) AF: 0.593 AC: 2859 AN: 4822

European-Finnish (FIN) AF: 0.555 AC: 5868 AN: 10566

Middle Eastern (MID) AF: 0.575 AC: 169 AN: 294

European-Non Finnish (NFE) AF: 0.557 AC: 37835 AN: 67972

Other (OTH) AF: 0.512 AC: 1079 AN: 2106

Alfa AF: 0.542 Hom.: 42248

Bravo AF: 0.494

Asia WGS AF: 0.647 AC: 2249 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	0.14
DANN	Benign	0.49
PhyloP100		-1.9

Splicing

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

Other links and lift over

dbSNP: rs560788; hg19: chr6-52830861;