rs4716272

Variant names:

• chr6-18497461-G-C
• rs4716272
• XR_926548.3:n.147+455G>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_926548.3(LOC105374955):​n.147+455G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.202 in 151,962 control chromosomes in the GnomAD database, including 3,167 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 0.20 (3167 hom., cov: 32)
• Consequence: LOC105374955 XR_926548.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.442
• Publications: 2 publications found

Genes affected

LOC105374955 (HGNC:):

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 (AMR) allele frequency at 95% confidence interval = 0.22 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: 0.202 AC: 30686 AN: 151844 Hom.: 3171 Cov.: 32

Gnomad AFR AF: 0.186

Gnomad AMI AF: 0.156

Gnomad AMR AF: 0.226

Gnomad ASJ AF: 0.147

Gnomad EAS AF: 0.0862

Gnomad SAS AF: 0.148

Gnomad FIN AF: 0.210

Gnomad MID AF: 0.245

Gnomad NFE AF: 0.221

Gnomad OTH AF: 0.207

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

GnomAD4 genome AF: 0.202 AC: 30694 AN: 151962 Hom.: 3167 Cov.: 32 AF XY: 0.201 AC XY: 14948 AN XY: 74258

African (AFR) AF: 0.185 AC: 7688 AN: 41446

American (AMR) AF: 0.226 AC: 3456 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.147 AC: 509 AN: 3472

East Asian (EAS) AF: 0.0859 AC: 443 AN: 5160

South Asian (SAS) AF: 0.148 AC: 711 AN: 4810

European-Finnish (FIN) AF: 0.210 AC: 2213 AN: 10520

Middle Eastern (MID) AF: 0.243 AC: 71 AN: 292

European-Non Finnish (NFE) AF: 0.221 AC: 15029 AN: 67960

Other (OTH) AF: 0.204 AC: 432 AN: 2114

Alfa AF: 0.209 Hom.: 421

Bravo AF: 0.208

Asia WGS AF: 0.118 AC: 410 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	8.3
DANN	Benign	0.61
PhyloP100		0.44

Splicing

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

Other links and lift over

dbSNP: rs4716272; hg19: chr6-18497692;