rs705469

Variant names:

• chr10-3616727-T-C
• rs705469
• ENST00000737075.1:n.205+9237A>G

Variant summary

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

The NR_131187.1(LOC105376360):​n.163-131961T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.344 in 146,982 control chromosomes in the GnomAD database, including 8,860 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 0.34 (8860 hom., cov: 24)
• Consequence: LOC105376360 NR_131187.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0970
• Publications: 6 publications found

Genes affected

ENSG00000296170 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.374 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NR_131187.1. 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
	LOC105376360	NR_131187.1		n.163-131961T>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000296170	ENST00000737075.1		n.205+9237A>G		intron	N/A
	ENSG00000296170	ENST00000737076.1		n.176+9237A>G		intron	N/A
	ENSG00000296170	ENST00000737077.1		n.180+9237A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.344 AC: 50518 AN: 146894 Hom.: 8862 Cov.: 24

Gnomad AFR AF: 0.303

Gnomad AMI AF: 0.274

Gnomad AMR AF: 0.378

Gnomad ASJ AF: 0.454

Gnomad EAS AF: 0.295

Gnomad SAS AF: 0.196

Gnomad FIN AF: 0.282

Gnomad MID AF: 0.373

Gnomad NFE AF: 0.378

Gnomad OTH AF: 0.358

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

GnomAD4 genome AF: 0.344 AC: 50509 AN: 146982 Hom.: 8860 Cov.: 24 AF XY: 0.337 AC XY: 24060 AN XY: 71442

African (AFR) AF: 0.302 AC: 12115 AN: 40056

American (AMR) AF: 0.377 AC: 5524 AN: 14638

Ashkenazi Jewish (ASJ) AF: 0.454 AC: 1564 AN: 3444

East Asian (EAS) AF: 0.295 AC: 1486 AN: 5030

South Asian (SAS) AF: 0.195 AC: 913 AN: 4676

European-Finnish (FIN) AF: 0.282 AC: 2570 AN: 9126

Middle Eastern (MID) AF: 0.359 AC: 102 AN: 284

European-Non Finnish (NFE) AF: 0.378 AC: 25265 AN: 66786

Other (OTH) AF: 0.354 AC: 723 AN: 2040

Alfa AF: 0.369 Hom.: 15093

Bravo AF: 0.355

Asia WGS AF: 0.242 AC: 835 AN: 3444

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.8
DANN	Benign	0.71
PhyloP100		0.097

Splicing

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

Other links and lift over

dbSNP: rs705469; hg19: chr10-3658919;