6-67093411-G-T

Variant names:

• chr6-67093411-G-T
• rs2502248

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: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.384

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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;