chr1-186715845-T-C

Variant names:

• chr1-186715845-T-C
• rs964570
• ENST00000742757.1:n.142+4876T>C

Variant summary

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

The ENST00000742757.1(ENSG00000296822):​n.142+4876T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.877 in 152,170 control chromosomes in the GnomAD database, including 58,882 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 0.88 (58882 hom., cov: 32)
• Consequence: ENSG00000296822 ENST00000742757.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.512
• Publications: 5 publications found

Genes affected

ENSG00000296822 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.974 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000742757.1. 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
	ENSG00000296822	ENST00000742757.1		n.142+4876T>C		intron	N/A
	ENSG00000296822	ENST00000742758.1		n.60-542T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.877 AC: 133328 AN: 152052 Hom.: 58851 Cov.: 32

Gnomad AFR AF: 0.755

Gnomad AMI AF: 0.847

Gnomad AMR AF: 0.944

Gnomad ASJ AF: 0.959

Gnomad EAS AF: 0.997

Gnomad SAS AF: 0.884

Gnomad FIN AF: 0.903

Gnomad MID AF: 0.946

Gnomad NFE AF: 0.917

Gnomad OTH AF: 0.895

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

GnomAD4 genome AF: 0.877 AC: 133405 AN: 152170 Hom.: 58882 Cov.: 32 AF XY: 0.879 AC XY: 65417 AN XY: 74408

African (AFR) AF: 0.755 AC: 31319 AN: 41478

American (AMR) AF: 0.944 AC: 14437 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.959 AC: 3325 AN: 3468

East Asian (EAS) AF: 0.997 AC: 5156 AN: 5174

South Asian (SAS) AF: 0.884 AC: 4265 AN: 4826

European-Finnish (FIN) AF: 0.903 AC: 9565 AN: 10596

Middle Eastern (MID) AF: 0.946 AC: 278 AN: 294

European-Non Finnish (NFE) AF: 0.917 AC: 62394 AN: 68016

Other (OTH) AF: 0.896 AC: 1895 AN: 2114

Alfa AF: 0.906 Hom.: 177385

Bravo AF: 0.876

Asia WGS AF: 0.928 AC: 3221 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	5.5
DANN	Benign	0.58
PhyloP100		0.51

Splicing

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

Other links and lift over

dbSNP: rs964570; hg19: chr1-186684977;