rs947008

Variant names:

• chr1-56262212-T-C
• rs947008
• ENST00000642129.1:n.*96-13012A>G

Variant summary

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

The ENST00000642129.1(ENSG00000284686):​n.*96-13012A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.391 in 151,966 control chromosomes in the GnomAD database, including 12,361 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 0.39 (12361 hom., cov: 32)
• Consequence: ENSG00000284686 ENST00000642129.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.169
• Publications: 2 publications found

Genes affected

ENSG00000284686 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.594 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000642129.1. 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
	ENSG00000284686	ENST00000642129.1		n.*96-13012A>G		intron	N/A	ENSP00000492927.1	A0A286YES4
	ENSG00000260971	ENST00000641035.1		n.556-13012A>G		intron	N/A
	ENSG00000284686	ENST00000641109.1		n.*322-13012A>G		intron	N/A	ENSP00000493138.1	A0A286YEZ7

Frequencies

GnomAD3 genomes AF: 0.391 AC: 59387 AN: 151848 Hom.: 12351 Cov.: 32

Gnomad AFR AF: 0.262

Gnomad AMI AF: 0.521

Gnomad AMR AF: 0.432

Gnomad ASJ AF: 0.342

Gnomad EAS AF: 0.612

Gnomad SAS AF: 0.347

Gnomad FIN AF: 0.503

Gnomad MID AF: 0.291

Gnomad NFE AF: 0.431

Gnomad OTH AF: 0.371

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

GnomAD4 genome AF: 0.391 AC: 59416 AN: 151966 Hom.: 12361 Cov.: 32 AF XY: 0.396 AC XY: 29405 AN XY: 74270

African (AFR) AF: 0.262 AC: 10865 AN: 41438

American (AMR) AF: 0.433 AC: 6609 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.342 AC: 1189 AN: 3472

East Asian (EAS) AF: 0.612 AC: 3142 AN: 5134

South Asian (SAS) AF: 0.347 AC: 1674 AN: 4820

European-Finnish (FIN) AF: 0.503 AC: 5307 AN: 10554

Middle Eastern (MID) AF: 0.299 AC: 88 AN: 294

European-Non Finnish (NFE) AF: 0.431 AC: 29290 AN: 67960

Other (OTH) AF: 0.369 AC: 779 AN: 2112

Alfa AF: 0.407 Hom.: 3909

Bravo AF: 0.384

Asia WGS AF: 0.431 AC: 1496 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.9
DANN	Benign	0.55
PhyloP100		0.17

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: rs947008;

hg19: chr1-56727884;

COSMIC: COSV73887238;