chr6-52971899-G-C

Position:

• chr6-52971899-G-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The variant allele was found at a frequency of 0.0298 in 152,298 control chromosomes in the GnomAD database, including 109 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 0.030 (109 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.216

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BS1: Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0298 (4533/152298) while in subpopulation NFE AF= 0.0473 (3216/68024). AF 95% confidence interval is 0.0459. There are 109 homozygotes in gnomad4. There are 2070 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 109 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.52971899G>C		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000291036	ENST00000448991.6	n.43+1208C>G		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.0298 AC: 4539 AN: 152180 Hom.: 110 Cov.: 32

Gnomad AFR AF: 0.00871

Gnomad AMI AF: 0.0581

Gnomad AMR AF: 0.0354

Gnomad ASJ AF: 0.0432

Gnomad EAS AF: 0.000193

Gnomad SAS AF: 0.00539

Gnomad FIN AF: 0.00565

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.0473

Gnomad OTH AF: 0.0411

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

GnomAD4 genome AF: 0.0298 AC: 4533 AN: 152298 Hom.: 109 Cov.: 32 AF XY: 0.0278 AC XY: 2070 AN XY: 74470

Gnomad4 AFR AF: 0.00869

Gnomad4 AMR AF: 0.0353

Gnomad4 ASJ AF: 0.0432

Gnomad4 EAS AF: 0.000193

Gnomad4 SAS AF: 0.00539

Gnomad4 FIN AF: 0.00565

Gnomad4 NFE AF: 0.0473

Gnomad4 OTH AF: 0.0402

Alfa AF: 0.0160 Hom.: 7

Bravo AF: 0.0316

Asia WGS AF: 0.00635 AC: 22 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	0.71
DANN	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17608261; hg19: chr6-52836697;