5-52660690-G-C

Variant names:

• chr5-52660690-G-C
• rs2406195
• ENST00000779689.1:n.454+7041C>G

Variant summary

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

The ENST00000779689.1(ENSG00000301558):​n.454+7041C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.187 in 152,066 control chromosomes in the GnomAD database, including 2,957 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 0.19 (2957 hom., cov: 32)
• Consequence: ENSG00000301558 ENST00000779689.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.50
• Publications: 2 publications found

Genes affected

ENSG00000301558 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.228 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000779689.1. You can select a different transcript below to see updated ACMG assignments.

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
	ENSG00000301558	ENST00000779689.1		n.454+7041C>G		intron	N/A
	ENSG00000301558	ENST00000779690.1		n.390+7041C>G		intron	N/A
	ENSG00000301558	ENST00000779691.1		n.306+7041C>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.187 AC: 28424 AN: 151948 Hom.: 2952 Cov.: 32

Gnomad AFR AF: 0.141

Gnomad AMI AF: 0.296

Gnomad AMR AF: 0.171

Gnomad ASJ AF: 0.223

Gnomad EAS AF: 0.00502

Gnomad SAS AF: 0.144

Gnomad FIN AF: 0.189

Gnomad MID AF: 0.215

Gnomad NFE AF: 0.231

Gnomad OTH AF: 0.196

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

GnomAD4 genome AF: 0.187 AC: 28456 AN: 152066 Hom.: 2957 Cov.: 32 AF XY: 0.183 AC XY: 13569 AN XY: 74312

African (AFR) AF: 0.142 AC: 5883 AN: 41498

American (AMR) AF: 0.171 AC: 2610 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.223 AC: 773 AN: 3464

East Asian (EAS) AF: 0.00503 AC: 26 AN: 5166

South Asian (SAS) AF: 0.144 AC: 694 AN: 4814

European-Finnish (FIN) AF: 0.189 AC: 1997 AN: 10578

Middle Eastern (MID) AF: 0.228 AC: 67 AN: 294

European-Non Finnish (NFE) AF: 0.231 AC: 15724 AN: 67958

Other (OTH) AF: 0.195 AC: 413 AN: 2116

Alfa AF: 0.0991 Hom.: 155

Bravo AF: 0.182

Asia WGS AF: 0.0870 AC: 303 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.22
DANN	Benign	0.41
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs2406195; hg19: chr5-51956524;