rs547136

Variant names:

• chr6-71500720-T-C
• rs547136

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 0.0454 in 152,192 control chromosomes in the GnomAD database, including 173 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 0.045 (173 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.31
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0528 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: 0.0454 AC: 6905 AN: 152074 Hom.: 172 Cov.: 32

Gnomad AFR AF: 0.0398

Gnomad AMI AF: 0.00439

Gnomad AMR AF: 0.0469

Gnomad ASJ AF: 0.0340

Gnomad EAS AF: 0.000772

Gnomad SAS AF: 0.0281

Gnomad FIN AF: 0.0437

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.0543

Gnomad OTH AF: 0.0555

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

GnomAD4 genome AF: 0.0454 AC: 6903 AN: 152192 Hom.: 173 Cov.: 32 AF XY: 0.0444 AC XY: 3307 AN XY: 74414

African (AFR) AF: 0.0396 AC: 1645 AN: 41526

American (AMR) AF: 0.0468 AC: 715 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.0340 AC: 118 AN: 3470

East Asian (EAS) AF: 0.000773 AC: 4 AN: 5172

South Asian (SAS) AF: 0.0278 AC: 134 AN: 4828

European-Finnish (FIN) AF: 0.0437 AC: 463 AN: 10604

Middle Eastern (MID) AF: 0.0340 AC: 10 AN: 294

European-Non Finnish (NFE) AF: 0.0543 AC: 3693 AN: 68004

Other (OTH) AF: 0.0554 AC: 117 AN: 2112

Alfa AF: 0.0536 Hom.: 390

Bravo AF: 0.0454

Asia WGS AF: 0.0150 AC: 51 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	6.2
DANN	Benign	0.57
PhyloP100		1.3

Splicing

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

Other links and lift over

dbSNP: rs547136; hg19: chr6-72210423;