chr1-24717620-C-T

Variant names:

• chr1-24717620-C-T
• rs4601530
• ENST00000825012.1:n.238-1435G>A

Variant summary

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

The ENST00000825012.1(ENSG00000307307):​n.238-1435G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.316 in 151,948 control chromosomes in the GnomAD database, including 7,988 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 0.32 (7988 hom., cov: 32)
  • Exomes 𝑓: 0.20 (0 hom.)
• Consequence: ENSG00000307307 ENST00000825012.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.133
• Publications: 53 publications found

Genes affected

ENSG00000307307 (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 (EAS) allele frequency at 95% confidence interval = 0.47 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000825012.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000307307	ENST00000825012.1		n.238-1435G>A		intron	N/A
	ENSG00000284699	ENST00000641176.1		n.*24C>T		downstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.316 AC: 47976 AN: 151818 Hom.: 7984 Cov.: 32

Gnomad AFR AF: 0.401

Gnomad AMI AF: 0.302

Gnomad AMR AF: 0.247

Gnomad ASJ AF: 0.374

Gnomad EAS AF: 0.486

Gnomad SAS AF: 0.467

Gnomad FIN AF: 0.277

Gnomad MID AF: 0.443

Gnomad NFE AF: 0.259

Gnomad OTH AF: 0.302

GnomAD4 exome AF: 0.200 AC: 2 AN: 10 Hom.: 0 Cov.: 0 AF XY: 0.167 AC XY: 1 AN XY: 6

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AF: 0.500 AC: 1 AN: 2

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 2

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.250 AC: 1 AN: 4

Other (OTH) AF: 0.00 AC: 0 AN: 2

GnomAD4 genome AF: 0.316 AC: 48020 AN: 151938 Hom.: 7988 Cov.: 32 AF XY: 0.319 AC XY: 23669 AN XY: 74256

African (AFR) AF: 0.402 AC: 16618 AN: 41386

American (AMR) AF: 0.247 AC: 3772 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.374 AC: 1297 AN: 3468

East Asian (EAS) AF: 0.486 AC: 2510 AN: 5166

South Asian (SAS) AF: 0.465 AC: 2239 AN: 4818

European-Finnish (FIN) AF: 0.277 AC: 2919 AN: 10556

Middle Eastern (MID) AF: 0.439 AC: 129 AN: 294

European-Non Finnish (NFE) AF: 0.259 AC: 17618 AN: 67968

Other (OTH) AF: 0.304 AC: 643 AN: 2116

Alfa AF: 0.279 Hom.: 21392

Bravo AF: 0.314

Asia WGS AF: 0.437 AC: 1521 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	3.7
DANN	Benign	0.41
PhyloP100		-0.13

Splicing

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

Other links and lift over

dbSNP: rs4601530; hg19: chr1-25044111;