6-68158440-G-T

Variant names:

• chr6-68158440-G-T
• rs777649

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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;