6-66669885-T-C

Variant names:

• chr6-66669885-T-C
• rs7764904

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 0.899 in 152,218 control chromosomes in the GnomAD database, including 61,965 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 0.90 (61965 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.02

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 = 0.945 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: 0.899 AC: 136764 AN: 152100 Hom.: 61936 Cov.: 32

Gnomad AFR AF: 0.779

Gnomad AMI AF: 0.965

Gnomad AMR AF: 0.931

Gnomad ASJ AF: 0.904

Gnomad EAS AF: 0.904

Gnomad SAS AF: 0.891

Gnomad FIN AF: 0.977

Gnomad MID AF: 0.886

Gnomad NFE AF: 0.952

Gnomad OTH AF: 0.918

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

GnomAD4 genome AF: 0.899 AC: 136849 AN: 152218 Hom.: 61965 Cov.: 32 AF XY: 0.900 AC XY: 66985 AN XY: 74426

Gnomad4 AFR AF: 0.779

Gnomad4 AMR AF: 0.931

Gnomad4 ASJ AF: 0.904

Gnomad4 EAS AF: 0.904

Gnomad4 SAS AF: 0.891

Gnomad4 FIN AF: 0.977

Gnomad4 NFE AF: 0.952

Gnomad4 OTH AF: 0.919

Alfa AF: 0.922 Hom.: 10964

Bravo AF: 0.892

Asia WGS AF: 0.902 AC: 3135 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.92
DANN	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7764904; hg19: chr6-67379778;