6-52971097-G-A

Position:

• chr6-52971097-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000448991.6(ENSG00000291036):​n.43+2010C>T variant causes a intron, non coding transcript 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: ENST00000448991.6 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.347

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000448991.6	n.43+2010C>T		intron_variant, non_coding_transcript_variant		3

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

Gnomad4 AFR AF: 0.381

Gnomad4 AMR AF: 0.437

Gnomad4 ASJ AF: 0.478

Gnomad4 EAS AF: 0.740

Gnomad4 SAS AF: 0.611

Gnomad4 FIN AF: 0.460

Gnomad4 NFE AF: 0.517

Gnomad4 OTH AF: 0.481

Alfa AF: 0.483 Hom.: 2307

Bravo AF: 0.471

Asia WGS AF: 0.640 AC: 2225 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs492146; hg19: chr6-52835895;