1-187692398-T-C

Variant names:

• chr1-187692398-T-C
• rs953554
• ENST00000767639.1:n.241-3797A>G

Variant summary

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

The ENST00000767639.1(ENSG00000299951):​n.241-3797A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.357 in 151,874 control chromosomes in the GnomAD database, including 11,326 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 0.36 (11326 hom., cov: 31)
• Consequence: ENSG00000299951 ENST00000767639.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.242
• Publications: 2 publications found

Genes affected

ENSG00000299951 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.472 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000767639.1. 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
	ENSG00000299951	ENST00000767639.1		n.241-3797A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.358 AC: 54254 AN: 151756 Hom.: 11331 Cov.: 31

Gnomad AFR AF: 0.178

Gnomad AMI AF: 0.427

Gnomad AMR AF: 0.335

Gnomad ASJ AF: 0.438

Gnomad EAS AF: 0.0150

Gnomad SAS AF: 0.275

Gnomad FIN AF: 0.490

Gnomad MID AF: 0.399

Gnomad NFE AF: 0.477

Gnomad OTH AF: 0.394

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

GnomAD4 genome AF: 0.357 AC: 54252 AN: 151874 Hom.: 11326 Cov.: 31 AF XY: 0.353 AC XY: 26183 AN XY: 74232

African (AFR) AF: 0.178 AC: 7374 AN: 41430

American (AMR) AF: 0.335 AC: 5099 AN: 15224

Ashkenazi Jewish (ASJ) AF: 0.438 AC: 1519 AN: 3468

East Asian (EAS) AF: 0.0151 AC: 78 AN: 5174

South Asian (SAS) AF: 0.276 AC: 1330 AN: 4818

European-Finnish (FIN) AF: 0.490 AC: 5169 AN: 10552

Middle Eastern (MID) AF: 0.405 AC: 119 AN: 294

European-Non Finnish (NFE) AF: 0.477 AC: 32353 AN: 67896

Other (OTH) AF: 0.390 AC: 823 AN: 2110

Alfa AF: 0.443 Hom.: 25961

Bravo AF: 0.338

Asia WGS AF: 0.146 AC: 513 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.2
DANN	Benign	0.69
PhyloP100		-0.24

Splicing

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

Other links and lift over

dbSNP: rs953554; hg19: chr1-187661530;