6-52971097-G-A

Variant names:

• chr6-52971097-G-A
• rs492146
• ENST00000448991.7:n.85+2010C>T

Variant summary

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

The ENST00000448991.7(ENSG00000291036):​n.85+2010C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.477 in 150,326 control chromosomes in the GnomAD database, including 17,669 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 0.48 (17669 hom., cov: 27)
• Consequence: ENSG00000291036 ENST00000448991.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.347
• Publications: 5 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=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.72 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000448991.7. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000291036	ENST00000448991.7	TSL:3	n.85+2010C>T		intron	N/A
	ENSG00000291036	ENST00000763228.1		n.48+2010C>T		intron	N/A
	ENSG00000291036	ENST00000763229.1		n.29+2010C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.477 AC: 71702 AN: 150210 Hom.: 17667 Cov.: 27

Gnomad AFR AF: 0.382

Gnomad AMI AF: 0.476

Gnomad AMR AF: 0.437

Gnomad ASJ AF: 0.478

Gnomad EAS AF: 0.740

Gnomad SAS AF: 0.610

Gnomad FIN AF: 0.460

Gnomad MID AF: 0.538

Gnomad NFE AF: 0.517

Gnomad OTH AF: 0.478

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

GnomAD4 genome AF: 0.477 AC: 71719 AN: 150326 Hom.: 17669 Cov.: 27 AF XY: 0.478 AC XY: 34984 AN XY: 73234

African (AFR) AF: 0.381 AC: 15539 AN: 40810

American (AMR) AF: 0.437 AC: 6635 AN: 15166

Ashkenazi Jewish (ASJ) AF: 0.478 AC: 1656 AN: 3462

East Asian (EAS) AF: 0.740 AC: 3767 AN: 5092

South Asian (SAS) AF: 0.611 AC: 2894 AN: 4734

European-Finnish (FIN) AF: 0.460 AC: 4667 AN: 10156

Middle Eastern (MID) AF: 0.544 AC: 160 AN: 294

European-Non Finnish (NFE) AF: 0.517 AC: 34963 AN: 67614

Other (OTH) AF: 0.481 AC: 1006 AN: 2090

Alfa AF: 0.480 Hom.: 2374

Bravo AF: 0.471

Asia WGS AF: 0.640 AC: 2225 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	5.2
DANN	Benign	0.60
PhyloP100		0.35

Splicing

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

Other links and lift over

dbSNP: rs492146; hg19: chr6-52835895;