chr1-56262212-T-C

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124904186	XR_007066107.1	n.13932-8319A>G		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000284686	ENST00000642129.1	n.*96-13012A>G		intron_variant	Intron 5 of 5			ENSP00000492927.1

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 v4.3

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

Other links and lift over

dbSNP: rs947008; hg19: chr1-56727884; COSMIC: COSV73887238;