6-151648063-C-T

Variant names:

• chr6-151648063-C-T
• rs77275268

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 0.066 in 152,168 control chromosomes in the GnomAD database, including 557 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 0.066 (557 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.881
• Publications: 10 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.297 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.0660 AC: 10042 AN: 152050 Hom.: 557 Cov.: 32

Gnomad AFR AF: 0.0314

Gnomad AMI AF: 0.0373

Gnomad AMR AF: 0.0615

Gnomad ASJ AF: 0.0881

Gnomad EAS AF: 0.310

Gnomad SAS AF: 0.0831

Gnomad FIN AF: 0.0262

Gnomad MID AF: 0.136

Gnomad NFE AF: 0.0729

Gnomad OTH AF: 0.0865

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

GnomAD4 genome AF: 0.0660 AC: 10042 AN: 152168 Hom.: 557 Cov.: 32 AF XY: 0.0655 AC XY: 4871 AN XY: 74402

African (AFR) AF: 0.0316 AC: 1310 AN: 41510

American (AMR) AF: 0.0614 AC: 939 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.0881 AC: 306 AN: 3472

East Asian (EAS) AF: 0.309 AC: 1597 AN: 5160

South Asian (SAS) AF: 0.0831 AC: 401 AN: 4824

European-Finnish (FIN) AF: 0.0262 AC: 278 AN: 10608

Middle Eastern (MID) AF: 0.136 AC: 40 AN: 294

European-Non Finnish (NFE) AF: 0.0729 AC: 4954 AN: 67990

Other (OTH) AF: 0.0866 AC: 183 AN: 2114

Alfa AF: 0.0572 Hom.: 144

Bravo AF: 0.0685

Asia WGS AF: 0.174 AC: 604 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.1
DANN	Benign	0.39
PhyloP100		-0.88

Splicing

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

Other links and lift over

dbSNP: rs77275268; hg19: chr6-151969198;