chr1-61584464-T-C

Variant names:

• chr1-61584464-T-C
• rs1933320
• ENST00000823956.1:n.145+8322A>G

Variant summary

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

The ENST00000823956.1(ENSG00000287224):​n.145+8322A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.924 in 152,270 control chromosomes in the GnomAD database, including 65,200 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 0.92 (65200 hom., cov: 32)
• Consequence: ENSG00000287224 ENST00000823956.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.469
• Publications: 1 publications found

Genes affected

ENSG00000287224 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.957 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000287224	ENST00000823956.1	n.145+8322A>G		intron_variant	Intron 2 of 2
ENSG00000287224	ENST00000823957.1	n.183-28565A>G		intron_variant	Intron 2 of 2
ENSG00000287224	ENST00000823958.1	n.250+8322A>G		intron_variant	Intron 3 of 3
ENSG00000287224	ENST00000823959.1	n.179+8322A>G		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.924 AC: 140574 AN: 152152 Hom.: 65158 Cov.: 32

Gnomad AFR AF: 0.864

Gnomad AMI AF: 0.866

Gnomad AMR AF: 0.852

Gnomad ASJ AF: 0.921

Gnomad EAS AF: 0.965

Gnomad SAS AF: 0.958

Gnomad FIN AF: 0.979

Gnomad MID AF: 0.930

Gnomad NFE AF: 0.963

Gnomad OTH AF: 0.928

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

GnomAD4 genome AF: 0.924 AC: 140673 AN: 152270 Hom.: 65200 Cov.: 32 AF XY: 0.924 AC XY: 68810 AN XY: 74466

African (AFR) AF: 0.864 AC: 35867 AN: 41528

American (AMR) AF: 0.852 AC: 13024 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.921 AC: 3197 AN: 3472

East Asian (EAS) AF: 0.965 AC: 5000 AN: 5180

South Asian (SAS) AF: 0.959 AC: 4627 AN: 4826

European-Finnish (FIN) AF: 0.979 AC: 10398 AN: 10618

Middle Eastern (MID) AF: 0.932 AC: 274 AN: 294

European-Non Finnish (NFE) AF: 0.963 AC: 65534 AN: 68036

Other (OTH) AF: 0.929 AC: 1964 AN: 2114

Alfa AF: 0.907 Hom.: 6932

Bravo AF: 0.909

Asia WGS AF: 0.950 AC: 3303 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.3
DANN	Benign	0.20
PhyloP100		0.47

Splicing

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

Other links and lift over

dbSNP: rs1933320; hg19: chr1-62050136;