rs951327

Variant names:

• chr3-176905130-T-C
• rs951327
• ENST00000807041.1:n.214-370A>G

Your query was ambiguous. Multiple possible variants found:

• chr3-176905130-T-C
• chr3-176905130-T-G

Variant summary

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

The ENST00000807041.1(ENSG00000304906):​n.214-370A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.41 in 152,024 control chromosomes in the GnomAD database, including 13,316 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 0.41 (13316 hom., cov: 32)
• Consequence: ENSG00000304906 ENST00000807041.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.681
• Publications: 3 publications found

Genes affected

ENSG00000304906 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.469 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000807041.1. 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
	ENSG00000304906	ENST00000807041.1		n.214-370A>G		intron	N/A
	ENSG00000304906	ENST00000807042.1		n.348-370A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.410 AC: 62257 AN: 151908 Hom.: 13328 Cov.: 32

Gnomad AFR AF: 0.271

Gnomad AMI AF: 0.373

Gnomad AMR AF: 0.379

Gnomad ASJ AF: 0.495

Gnomad EAS AF: 0.423

Gnomad SAS AF: 0.450

Gnomad FIN AF: 0.542

Gnomad MID AF: 0.363

Gnomad NFE AF: 0.473

Gnomad OTH AF: 0.417

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

GnomAD4 genome AF: 0.410 AC: 62260 AN: 152024 Hom.: 13316 Cov.: 32 AF XY: 0.411 AC XY: 30542 AN XY: 74342

African (AFR) AF: 0.271 AC: 11224 AN: 41470

American (AMR) AF: 0.379 AC: 5788 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.495 AC: 1715 AN: 3464

East Asian (EAS) AF: 0.423 AC: 2187 AN: 5176

South Asian (SAS) AF: 0.449 AC: 2163 AN: 4822

European-Finnish (FIN) AF: 0.542 AC: 5720 AN: 10558

Middle Eastern (MID) AF: 0.360 AC: 105 AN: 292

European-Non Finnish (NFE) AF: 0.473 AC: 32144 AN: 67942

Other (OTH) AF: 0.414 AC: 874 AN: 2112

Alfa AF: 0.433 Hom.: 7029

Bravo AF: 0.391

Asia WGS AF: 0.436 AC: 1508 AN: 3460

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	7.6
DANN	Benign	0.74
PhyloP100		0.68

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs951327;

hg19: chr3-176622918;