chr4-87732464-A-G

Variant names:

• chr4-87732464-A-G
• rs2627690
• ENST00000503993.1:n.93+1400T>C

Variant summary

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

The ENST00000503993.1(ENSG00000249001):​n.93+1400T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.711 in 152,062 control chromosomes in the GnomAD database, including 38,730 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 0.71 (38729 hom., cov: 31)
  • Exomes 𝑓: 1.0 (1 hom.)
• Consequence: ENSG00000249001 ENST00000503993.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.409
• Publications: 5 publications found

Genes affected

ENSG00000249001 (HGNC:58144):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.853 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DMP1-AS1	NR_198971.1	n.-50T>C		upstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000249001	ENST00000503993.1	n.93+1400T>C		intron_variant	Intron 1 of 2	2
ENSG00000249001	ENST00000507894.2	n.107+622T>C		intron_variant	Intron 1 of 3	3
ENSG00000249001	ENST00000701198.2	n.93-18T>C		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.711 AC: 108063 AN: 151942 Hom.: 38700 Cov.: 31

Gnomad AFR AF: 0.716

Gnomad AMI AF: 0.600

Gnomad AMR AF: 0.763

Gnomad ASJ AF: 0.495

Gnomad EAS AF: 0.874

Gnomad SAS AF: 0.656

Gnomad FIN AF: 0.697

Gnomad MID AF: 0.687

Gnomad NFE AF: 0.703

Gnomad OTH AF: 0.707

GnomAD4 exome AF: 1.00 AC: 2 AN: 2 Hom.: 1 AF XY: 1.00 AC XY: 2 AN XY: 2

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 1.00 AC: 2 AN: 2

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AC: 0 AN: 0

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.711 AC: 108137 AN: 152060 Hom.: 38729 Cov.: 31 AF XY: 0.711 AC XY: 52832 AN XY: 74332

African (AFR) AF: 0.716 AC: 29666 AN: 41460

American (AMR) AF: 0.763 AC: 11659 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.495 AC: 1718 AN: 3472

East Asian (EAS) AF: 0.874 AC: 4521 AN: 5172

South Asian (SAS) AF: 0.656 AC: 3157 AN: 4812

European-Finnish (FIN) AF: 0.697 AC: 7363 AN: 10560

Middle Eastern (MID) AF: 0.687 AC: 202 AN: 294

European-Non Finnish (NFE) AF: 0.703 AC: 47806 AN: 67990

Other (OTH) AF: 0.710 AC: 1500 AN: 2112

Alfa AF: 0.696 Hom.: 18939

Bravo AF: 0.719

Asia WGS AF: 0.787 AC: 2738 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.4
DANN	Benign	0.70
PhyloP100		-0.41

Splicing

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

Other links and lift over

dbSNP: rs2627690; hg19: chr4-88653616;