chr6-68158440-G-T

Position:

• chr6-68158440-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 0.399 in 151,928 control chromosomes in the GnomAD database, including 12,350 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 0.40 (12350 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0750

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.428 is higher than 0.05.

Transcripts

RefSeq

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

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.399 AC: 60562 AN: 151810 Hom.: 12337 Cov.: 32

Gnomad AFR AF: 0.353

Gnomad AMI AF: 0.441

Gnomad AMR AF: 0.305

Gnomad ASJ AF: 0.485

Gnomad EAS AF: 0.421

Gnomad SAS AF: 0.418

Gnomad FIN AF: 0.450

Gnomad MID AF: 0.415

Gnomad NFE AF: 0.433

Gnomad OTH AF: 0.386

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

GnomAD4 genome AF: 0.399 AC: 60606 AN: 151928 Hom.: 12350 Cov.: 32 AF XY: 0.398 AC XY: 29575 AN XY: 74236

Gnomad4 AFR AF: 0.353

Gnomad4 AMR AF: 0.304

Gnomad4 ASJ AF: 0.485

Gnomad4 EAS AF: 0.420

Gnomad4 SAS AF: 0.418

Gnomad4 FIN AF: 0.450

Gnomad4 NFE AF: 0.433

Gnomad4 OTH AF: 0.388

Alfa AF: 0.415 Hom.: 26282

Bravo AF: 0.383

Asia WGS AF: 0.384 AC: 1331 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	1.9
DANN	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs777649; hg19: chr6-68868332;