chr6-65888301-G-A

Position:

• chr6-65888301-G-A

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 0.337 in 152,000 control chromosomes in the GnomAD database, including 9,956 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 0.34 (9956 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.190

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.447 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.65888301G>A		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.338 AC: 51285 AN: 151880 Hom.: 9957 Cov.: 32

Gnomad AFR AF: 0.155

Gnomad AMI AF: 0.491

Gnomad AMR AF: 0.305

Gnomad ASJ AF: 0.484

Gnomad EAS AF: 0.152

Gnomad SAS AF: 0.295

Gnomad FIN AF: 0.409

Gnomad MID AF: 0.446

Gnomad NFE AF: 0.451

Gnomad OTH AF: 0.372

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

GnomAD4 genome AF: 0.337 AC: 51290 AN: 152000 Hom.: 9956 Cov.: 32 AF XY: 0.332 AC XY: 24626 AN XY: 74272

Gnomad4 AFR AF: 0.155

Gnomad4 AMR AF: 0.304

Gnomad4 ASJ AF: 0.484

Gnomad4 EAS AF: 0.152

Gnomad4 SAS AF: 0.296

Gnomad4 FIN AF: 0.409

Gnomad4 NFE AF: 0.451

Gnomad4 OTH AF: 0.369

Alfa AF: 0.437 Hom.: 15383

Bravo AF: 0.322

Asia WGS AF: 0.224 AC: 782 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.6
DANN	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10455590; hg19: chr6-66598194;