rs4709845

Variant names:

• chr6-164479565-G-A
• rs4709845
• XR_001744460.3:n.250-28135G>A

Variant summary

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

The XR_001744460.3(LOC107986667):​n.250-28135G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.17 in 151,082 control chromosomes in the GnomAD database, including 2,404 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 0.17 (2404 hom., cov: 31)
• Consequence: LOC107986667 XR_001744460.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.184
• Publications: 6 publications found

Genes affected

LOC107986667 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.343 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: 0.170 AC: 25618 AN: 150970 Hom.: 2398 Cov.: 31

Gnomad AFR AF: 0.159

Gnomad AMI AF: 0.127

Gnomad AMR AF: 0.249

Gnomad ASJ AF: 0.139

Gnomad EAS AF: 0.357

Gnomad SAS AF: 0.293

Gnomad FIN AF: 0.120

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.146

Gnomad OTH AF: 0.160

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

GnomAD4 genome AF: 0.170 AC: 25655 AN: 151082 Hom.: 2404 Cov.: 31 AF XY: 0.173 AC XY: 12764 AN XY: 73758

African (AFR) AF: 0.159 AC: 6572 AN: 41292

American (AMR) AF: 0.249 AC: 3769 AN: 15128

Ashkenazi Jewish (ASJ) AF: 0.139 AC: 480 AN: 3462

East Asian (EAS) AF: 0.357 AC: 1829 AN: 5122

South Asian (SAS) AF: 0.292 AC: 1400 AN: 4788

European-Finnish (FIN) AF: 0.120 AC: 1243 AN: 10324

Middle Eastern (MID) AF: 0.110 AC: 32 AN: 292

European-Non Finnish (NFE) AF: 0.146 AC: 9871 AN: 67660

Other (OTH) AF: 0.163 AC: 343 AN: 2102

Alfa AF: 0.165 Hom.: 5550

Bravo AF: 0.177

Asia WGS AF: 0.304 AC: 1055 AN: 3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	5.0
DANN	Benign	0.78
PhyloP100		0.18

Splicing

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

Other links and lift over

dbSNP: rs4709845; hg19: chr6-164900598; COSMIC: COSV69432913;