rs4714772

Variant names:

• chr6-44239380-A-C
• rs4714772

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 0.153 in 151,390 control chromosomes in the GnomAD database, including 2,322 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 0.15 (2322 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.623
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.351 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: 0.153 AC: 23197 AN: 151272 Hom.: 2322 Cov.: 31

Gnomad AFR AF: 0.0439

Gnomad AMI AF: 0.202

Gnomad AMR AF: 0.240

Gnomad ASJ AF: 0.132

Gnomad EAS AF: 0.365

Gnomad SAS AF: 0.294

Gnomad FIN AF: 0.184

Gnomad MID AF: 0.136

Gnomad NFE AF: 0.170

Gnomad OTH AF: 0.151

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

GnomAD4 genome AF: 0.153 AC: 23195 AN: 151390 Hom.: 2322 Cov.: 31 AF XY: 0.158 AC XY: 11652 AN XY: 73904

African (AFR) AF: 0.0438 AC: 1806 AN: 41252

American (AMR) AF: 0.240 AC: 3636 AN: 15154

Ashkenazi Jewish (ASJ) AF: 0.132 AC: 458 AN: 3464

East Asian (EAS) AF: 0.365 AC: 1879 AN: 5150

South Asian (SAS) AF: 0.294 AC: 1402 AN: 4770

European-Finnish (FIN) AF: 0.184 AC: 1917 AN: 10438

Middle Eastern (MID) AF: 0.133 AC: 39 AN: 294

European-Non Finnish (NFE) AF: 0.170 AC: 11557 AN: 67856

Other (OTH) AF: 0.151 AC: 318 AN: 2104

Alfa AF: 0.164 Hom.: 2976

Bravo AF: 0.154

Asia WGS AF: 0.307 AC: 1068 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	0.095
DANN	Benign	0.85
PhyloP100		-0.62

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs4714772;

hg19: chr6-44207117;