6-95519536-T-C

Position:

• chr6-95519536-T-C

Variant summary

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

The variant allele was found at a frequency of 0.848 in 152,176 control chromosomes in the GnomAD database, including 55,155 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 0.85 (55155 hom., cov: 33)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.70

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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 = 0.928 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.95519536T>C		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.848 AC: 128977 AN: 152060 Hom.: 55109 Cov.: 33

Gnomad AFR AF: 0.928

Gnomad AMI AF: 0.895

Gnomad AMR AF: 0.699

Gnomad ASJ AF: 0.826

Gnomad EAS AF: 0.951

Gnomad SAS AF: 0.829

Gnomad FIN AF: 0.778

Gnomad MID AF: 0.842

Gnomad NFE AF: 0.838

Gnomad OTH AF: 0.835

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

GnomAD4 genome AF: 0.848 AC: 129080 AN: 152176 Hom.: 55155 Cov.: 33 AF XY: 0.842 AC XY: 62631 AN XY: 74368

Gnomad4 AFR AF: 0.929

Gnomad4 AMR AF: 0.699

Gnomad4 ASJ AF: 0.826

Gnomad4 EAS AF: 0.951

Gnomad4 SAS AF: 0.829

Gnomad4 FIN AF: 0.778

Gnomad4 NFE AF: 0.838

Gnomad4 OTH AF: 0.837

Alfa AF: 0.840 Hom.: 24436

Bravo AF: 0.846

Asia WGS AF: 0.877 AC: 3049 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	0.42
DANN	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2380220; hg19: chr6-95967412;