chr6-66417458-T-C

Variant names:

• chr6-66417458-T-C
• rs10223661

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 0.126 in 151,670 control chromosomes in the GnomAD database, including 1,356 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 0.13 (1356 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.535
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.172 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.126 AC: 19123 AN: 151552 Hom.: 1355 Cov.: 32

Gnomad AFR AF: 0.175

Gnomad AMI AF: 0.0976

Gnomad AMR AF: 0.0693

Gnomad ASJ AF: 0.115

Gnomad EAS AF: 0.0113

Gnomad SAS AF: 0.0424

Gnomad FIN AF: 0.148

Gnomad MID AF: 0.104

Gnomad NFE AF: 0.122

Gnomad OTH AF: 0.113

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

GnomAD4 genome AF: 0.126 AC: 19139 AN: 151670 Hom.: 1356 Cov.: 32 AF XY: 0.126 AC XY: 9327 AN XY: 74152

African (AFR) AF: 0.175 AC: 7268 AN: 41440

American (AMR) AF: 0.0691 AC: 1050 AN: 15186

Ashkenazi Jewish (ASJ) AF: 0.115 AC: 397 AN: 3458

East Asian (EAS) AF: 0.0113 AC: 58 AN: 5130

South Asian (SAS) AF: 0.0429 AC: 207 AN: 4830

European-Finnish (FIN) AF: 0.148 AC: 1573 AN: 10598

Middle Eastern (MID) AF: 0.0986 AC: 29 AN: 294

European-Non Finnish (NFE) AF: 0.122 AC: 8232 AN: 67716

Other (OTH) AF: 0.112 AC: 236 AN: 2106

Alfa AF: 0.130 Hom.: 184

Bravo AF: 0.122

Asia WGS AF: 0.0430 AC: 149 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	5.4
DANN	Benign	0.53
PhyloP100		0.54

Splicing

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

Other links and lift over

dbSNP: rs10223661; hg19: chr6-67127351;