chr6-67093411-G-T

Position:

• chr6-67093411-G-T

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 0.635 in 151,872 control chromosomes in the GnomAD database, including 31,417 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 0.63 (31417 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.384

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 (AFR) allele frequency at 95% confidence interval = 0.783 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.67093411G>T		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.634 AC: 96266 AN: 151754 Hom.: 31371 Cov.: 32

Gnomad AFR AF: 0.789

Gnomad AMI AF: 0.684

Gnomad AMR AF: 0.620

Gnomad ASJ AF: 0.638

Gnomad EAS AF: 0.602

Gnomad SAS AF: 0.663

Gnomad FIN AF: 0.553

Gnomad MID AF: 0.630

Gnomad NFE AF: 0.555

Gnomad OTH AF: 0.643

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

GnomAD4 genome AF: 0.635 AC: 96370 AN: 151872 Hom.: 31417 Cov.: 32 AF XY: 0.636 AC XY: 47234 AN XY: 74218

Gnomad4 AFR AF: 0.790

Gnomad4 AMR AF: 0.620

Gnomad4 ASJ AF: 0.638

Gnomad4 EAS AF: 0.602

Gnomad4 SAS AF: 0.662

Gnomad4 FIN AF: 0.553

Gnomad4 NFE AF: 0.555

Gnomad4 OTH AF: 0.647

Alfa AF: 0.597 Hom.: 3479

Bravo AF: 0.644

Asia WGS AF: 0.657 AC: 2283 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	8.2
DANN	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2502248; hg19: chr6-67803304; COSMIC: COSV69401077;