rs9378212

Variant names:

• chr6-32477914-C-G
• rs9378212
• ENST00000829864.1:n.273+3705C>G

Your query was ambiguous. Multiple possible variants found:

• chr6-32477914-C-G
• chr6-32477914-C-T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The ENST00000829864.1(ENSG00000307923):​n.273+3705C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.104 in 128,482 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 0.10 (0 hom., cov: 36)
• Consequence: ENSG00000307923 ENST00000829864.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.06
• Publications: 21 publications found

Genes affected

ENSG00000307923 (HGNC:):

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Variant has high frequency in the AFR (0.146) population. However there is too low homozygotes in high coverage region: (expected more than 345, got 0).
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).

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
ENSG00000307923	ENST00000829864.1	n.273+3705C>G		intron_variant	Intron 2 of 2
ENSG00000307923	ENST00000829865.1	n.270-1222C>G		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.104 AC: 13320 AN: 128368 Hom.: 0 Cov.: 36

Gnomad AFR AF: 0.149

Gnomad AMI AF: 0.0405

Gnomad AMR AF: 0.0909

Gnomad ASJ AF: 0.0929

Gnomad EAS AF: 0.0727

Gnomad SAS AF: 0.103

Gnomad FIN AF: 0.0659

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.0910

Gnomad OTH AF: 0.110

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

GnomAD4 genome AF: 0.104 AC: 13334 AN: 128482 Hom.: 0 Cov.: 36 AF XY: 0.104 AC XY: 6539 AN XY: 62998

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5.

African (AFR) AF: 0.149 AC: 4885 AN: 32760

American (AMR) AF: 0.0909 AC: 1214 AN: 13362

Ashkenazi Jewish (ASJ) AF: 0.0929 AC: 289 AN: 3112

East Asian (EAS) AF: 0.0725 AC: 314 AN: 4334

South Asian (SAS) AF: 0.104 AC: 413 AN: 3984

European-Finnish (FIN) AF: 0.0659 AC: 615 AN: 9336

Middle Eastern (MID) AF: 0.147 AC: 33 AN: 224

European-Non Finnish (NFE) AF: 0.0910 AC: 5340 AN: 58708

Other (OTH) AF: 0.109 AC: 196 AN: 1798

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5. (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.

Alfa AF: 0.00843 Hom.: 5238

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.0
DANN	Benign	0.31
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs9378212; hg19: chr6-32445691;