chr6-145196271-C-A

Variant names:

• chr6-145196271-C-A
• rs4896780

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 0.431 in 151,940 control chromosomes in the GnomAD database, including 19,846 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 0.43 (19846 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.75
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.839 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: 0.430 AC: 65310 AN: 151822 Hom.: 19782 Cov.: 31

Gnomad AFR AF: 0.846

Gnomad AMI AF: 0.249

Gnomad AMR AF: 0.487

Gnomad ASJ AF: 0.315

Gnomad EAS AF: 0.528

Gnomad SAS AF: 0.309

Gnomad FIN AF: 0.228

Gnomad MID AF: 0.217

Gnomad NFE AF: 0.207

Gnomad OTH AF: 0.407

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

GnomAD4 genome AF: 0.431 AC: 65444 AN: 151940 Hom.: 19846 Cov.: 31 AF XY: 0.433 AC XY: 32130 AN XY: 74250

African (AFR) AF: 0.847 AC: 35112 AN: 41462

American (AMR) AF: 0.488 AC: 7449 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.315 AC: 1093 AN: 3472

East Asian (EAS) AF: 0.528 AC: 2717 AN: 5150

South Asian (SAS) AF: 0.309 AC: 1488 AN: 4814

European-Finnish (FIN) AF: 0.228 AC: 2400 AN: 10508

Middle Eastern (MID) AF: 0.229 AC: 67 AN: 292

European-Non Finnish (NFE) AF: 0.207 AC: 14035 AN: 67946

Other (OTH) AF: 0.406 AC: 856 AN: 2108

Alfa AF: 0.293 Hom.: 17871

Bravo AF: 0.469

Asia WGS AF: 0.446 AC: 1552 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.78
DANN	Benign	0.20
PhyloP100		-1.7

Splicing

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

Other links and lift over

dbSNP: rs4896780; hg19: chr6-145517407;