6-66417119-G-T

Variant names:

• chr6-66417119-G-T
• rs10223766

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.119 in 151,626 control chromosomes in the GnomAD database, including 1,216 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 0.12 (1216 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00200
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.151 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.119 AC: 18101 AN: 151508 Hom.: 1216 Cov.: 32

Gnomad AFR AF: 0.154

Gnomad AMI AF: 0.0976

Gnomad AMR AF: 0.0640

Gnomad ASJ AF: 0.113

Gnomad EAS AF: 0.0109

Gnomad SAS AF: 0.0422

Gnomad FIN AF: 0.148

Gnomad MID AF: 0.0886

Gnomad NFE AF: 0.121

Gnomad OTH AF: 0.109

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

GnomAD4 genome AF: 0.119 AC: 18114 AN: 151626 Hom.: 1216 Cov.: 32 AF XY: 0.119 AC XY: 8798 AN XY: 74092

African (AFR) AF: 0.154 AC: 6374 AN: 41438

American (AMR) AF: 0.0639 AC: 968 AN: 15154

Ashkenazi Jewish (ASJ) AF: 0.113 AC: 390 AN: 3458

East Asian (EAS) AF: 0.0109 AC: 56 AN: 5126

South Asian (SAS) AF: 0.0427 AC: 206 AN: 4826

European-Finnish (FIN) AF: 0.148 AC: 1565 AN: 10582

Middle Eastern (MID) AF: 0.0816 AC: 24 AN: 294

European-Non Finnish (NFE) AF: 0.121 AC: 8215 AN: 67724

Other (OTH) AF: 0.107 AC: 227 AN: 2112

Alfa AF: 0.125 Hom.: 167

Bravo AF: 0.115

Asia WGS AF: 0.0420 AC: 145 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.6
DANN	Benign	0.74
PhyloP100		-0.0020

Splicing

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

Other links and lift over

dbSNP: rs10223766; hg19: chr6-67127012;