rs187954

Variant names:

• chr1-29661757-C-A
• rs187954
• ENST00000772656.1:n.174-17362C>A

Your query was ambiguous. Multiple possible variants found:

• chr1-29661757-C-A
• chr1-29661757-C-G

Variant summary

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

The ENST00000772656.1(ENSG00000300547):​n.174-17362C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.458 in 151,918 control chromosomes in the GnomAD database, including 16,149 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 0.46 (16149 hom., cov: 32)
• Consequence: ENSG00000300547 ENST00000772656.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.977
• Publications: 3 publications found

Genes affected

ENSG00000300547 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.599 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107984934	XR_001737956.1	n.221-17362C>A		intron_variant	Intron 1 of 3
LOC107984934	XR_001737957.1	n.221-17362C>A		intron_variant	Intron 1 of 4
LOC107984934	XR_001737958.2	n.221-17362C>A		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000300547	ENST00000772656.1	n.174-17362C>A		intron_variant	Intron 2 of 4
ENSG00000300547	ENST00000772657.1	n.188-17362C>A		intron_variant	Intron 2 of 3
ENSG00000300547	ENST00000772658.1	n.171-17362C>A		intron_variant	Intron 2 of 4

Frequencies

GnomAD3 genomes AF: 0.458 AC: 69555 AN: 151802 Hom.: 16130 Cov.: 32

Gnomad AFR AF: 0.449

Gnomad AMI AF: 0.532

Gnomad AMR AF: 0.509

Gnomad ASJ AF: 0.360

Gnomad EAS AF: 0.618

Gnomad SAS AF: 0.569

Gnomad FIN AF: 0.400

Gnomad MID AF: 0.383

Gnomad NFE AF: 0.445

Gnomad OTH AF: 0.468

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

GnomAD4 genome AF: 0.458 AC: 69620 AN: 151918 Hom.: 16149 Cov.: 32 AF XY: 0.460 AC XY: 34191 AN XY: 74254

African (AFR) AF: 0.449 AC: 18625 AN: 41458

American (AMR) AF: 0.509 AC: 7778 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.360 AC: 1249 AN: 3470

East Asian (EAS) AF: 0.617 AC: 3180 AN: 5152

South Asian (SAS) AF: 0.571 AC: 2747 AN: 4814

European-Finnish (FIN) AF: 0.400 AC: 4214 AN: 10548

Middle Eastern (MID) AF: 0.381 AC: 112 AN: 294

European-Non Finnish (NFE) AF: 0.445 AC: 30242 AN: 67884

Other (OTH) AF: 0.470 AC: 991 AN: 2110

Alfa AF: 0.453 Hom.: 9223

Bravo AF: 0.468

Asia WGS AF: 0.607 AC: 2109 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	6.9
DANN	Benign	0.53
PhyloP100		-0.98

Splicing

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

Other links and lift over

dbSNP: rs187954; hg19: chr1-30134604; COSMIC: COSV59933877;