6-144967129-A-C

Variant names:

• chr6-144967129-A-C
• rs7760387

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 0.261 in 151,972 control chromosomes in the GnomAD database, including 7,587 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 0.26 (7587 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.681
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.525 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: 0.260 AC: 39542 AN: 151854 Hom.: 7565 Cov.: 32

Gnomad AFR AF: 0.509

Gnomad AMI AF: 0.185

Gnomad AMR AF: 0.201

Gnomad ASJ AF: 0.130

Gnomad EAS AF: 0.541

Gnomad SAS AF: 0.385

Gnomad FIN AF: 0.160

Gnomad MID AF: 0.304

Gnomad NFE AF: 0.116

Gnomad OTH AF: 0.258

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

GnomAD4 genome AF: 0.261 AC: 39613 AN: 151972 Hom.: 7587 Cov.: 32 AF XY: 0.267 AC XY: 19828 AN XY: 74298

African (AFR) AF: 0.509 AC: 21081 AN: 41388

American (AMR) AF: 0.201 AC: 3075 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.130 AC: 450 AN: 3470

East Asian (EAS) AF: 0.542 AC: 2792 AN: 5156

South Asian (SAS) AF: 0.384 AC: 1849 AN: 4814

European-Finnish (FIN) AF: 0.160 AC: 1688 AN: 10580

Middle Eastern (MID) AF: 0.310 AC: 91 AN: 294

European-Non Finnish (NFE) AF: 0.116 AC: 7864 AN: 67984

Other (OTH) AF: 0.263 AC: 554 AN: 2108

Alfa AF: 0.173 Hom.: 10014

Bravo AF: 0.275

Asia WGS AF: 0.439 AC: 1529 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.90
DANN	Benign	0.34
PhyloP100		-0.68

Splicing

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

Other links and lift over

dbSNP: rs7760387; hg19: chr6-145288265;