chr1-44032791-G-C

Variant names:

• chr1-44032791-G-C
• rs2477618
• ENST00000623351.1:n.115+2234G>C

Variant summary

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

The ENST00000623351.1(ENSG00000230615):​n.115+2234G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.138 in 152,192 control chromosomes in the GnomAD database, including 2,098 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 0.14 (2098 hom., cov: 32)
• Consequence: ENSG00000230615 ENST00000623351.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.395
• Publications: 2 publications found

Genes affected

ENSG00000230615 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.68).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.27 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107984948	XR_001738029.2	n.144+2234G>C		intron_variant	Intron 1 of 1
LOC107984948	XR_007066054.1	n.136+2242G>C		intron_variant	Intron 1 of 1
LOC124904168	XR_007066055.1	n.940-64C>G		intron_variant	Intron 3 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000230615	ENST00000623351.1	n.115+2234G>C		intron_variant	Intron 1 of 1	3
ENSG00000230615	ENST00000624869.1	n.25+2323G>C		intron_variant	Intron 1 of 1	5
ENSG00000230615	ENST00000657086.3	n.144+2234G>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.138 AC: 20952 AN: 152072 Hom.: 2090 Cov.: 32

Gnomad AFR AF: 0.274

Gnomad AMI AF: 0.0296

Gnomad AMR AF: 0.178

Gnomad ASJ AF: 0.101

Gnomad EAS AF: 0.0641

Gnomad SAS AF: 0.0611

Gnomad FIN AF: 0.0676

Gnomad MID AF: 0.123

Gnomad NFE AF: 0.0717

Gnomad OTH AF: 0.126

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

GnomAD4 genome AF: 0.138 AC: 21001 AN: 152192 Hom.: 2098 Cov.: 32 AF XY: 0.137 AC XY: 10183 AN XY: 74408

African (AFR) AF: 0.274 AC: 11382 AN: 41484

American (AMR) AF: 0.178 AC: 2717 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.101 AC: 350 AN: 3468

East Asian (EAS) AF: 0.0642 AC: 332 AN: 5168

South Asian (SAS) AF: 0.0612 AC: 295 AN: 4824

European-Finnish (FIN) AF: 0.0676 AC: 717 AN: 10606

Middle Eastern (MID) AF: 0.129 AC: 38 AN: 294

European-Non Finnish (NFE) AF: 0.0717 AC: 4877 AN: 68024

Other (OTH) AF: 0.126 AC: 266 AN: 2116

Alfa AF: 0.102 Hom.: 132

Bravo AF: 0.154

Asia WGS AF: 0.0700 AC: 241 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.68
CADD	Benign	4.5
DANN	Benign	0.69
PhyloP100		0.40

Splicing

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

Other links and lift over

dbSNP: rs2477618; hg19: chr1-44498463;