rs9312169

Variant names:

• chr4-67142250-A-C
• rs9312169
• ENST00000754279.1:n.471-849T>G

Your query was ambiguous. Multiple possible variants found:

• chr4-67142250-A-C
• chr4-67142250-A-T

Variant summary

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

The ENST00000754279.1(ENSG00000298266):​n.471-849T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.182 in 152,092 control chromosomes in the GnomAD database, including 2,644 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 0.18 (2644 hom., cov: 32)
• Consequence: ENSG00000298266 ENST00000754279.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.514
• Publications: 2 publications found

Genes affected

ENSG00000298266 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.223 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000298266	ENST00000754279.1	n.471-849T>G		intron_variant	Intron 3 of 3
ENSG00000298266	ENST00000754284.1	n.84-849T>G		intron_variant	Intron 1 of 1
ENSG00000298266	ENST00000754291.1	n.607-849T>G		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.182 AC: 27628 AN: 151974 Hom.: 2627 Cov.: 32

Gnomad AFR AF: 0.226

Gnomad AMI AF: 0.0855

Gnomad AMR AF: 0.133

Gnomad ASJ AF: 0.185

Gnomad EAS AF: 0.0866

Gnomad SAS AF: 0.104

Gnomad FIN AF: 0.209

Gnomad MID AF: 0.196

Gnomad NFE AF: 0.176

Gnomad OTH AF: 0.171

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

GnomAD4 genome AF: 0.182 AC: 27677 AN: 152092 Hom.: 2644 Cov.: 32 AF XY: 0.181 AC XY: 13425 AN XY: 74366

African (AFR) AF: 0.227 AC: 9401 AN: 41454

American (AMR) AF: 0.133 AC: 2027 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.185 AC: 643 AN: 3472

East Asian (EAS) AF: 0.0861 AC: 446 AN: 5182

South Asian (SAS) AF: 0.104 AC: 499 AN: 4808

European-Finnish (FIN) AF: 0.209 AC: 2212 AN: 10584

Middle Eastern (MID) AF: 0.204 AC: 60 AN: 294

European-Non Finnish (NFE) AF: 0.176 AC: 11954 AN: 67994

Other (OTH) AF: 0.169 AC: 357 AN: 2112

Alfa AF: 0.118 Hom.: 254

Bravo AF: 0.179

Asia WGS AF: 0.120 AC: 418 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.31
DANN	Benign	0.51
PhyloP100		-0.51

Splicing

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

Other links and lift over

dbSNP: rs9312169; hg19: chr4-68007968;