rs1449984

Variant names:

• chr2-23191780-A-G
• rs1449984
• ENST00000440785.1:n.248+7029T>C

Variant summary

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

The ENST00000440785.1(ENSG00000232451):​n.248+7029T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.261 in 152,146 control chromosomes in the GnomAD database, including 5,533 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 0.26 (5533 hom., cov: 32)
• Consequence: ENSG00000232451 ENST00000440785.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0550
• Publications: 10 publications found

Genes affected

ENSG00000232451 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.314 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107985792	NR_171639.1	n.121+7029T>C		intron_variant	Intron 1 of 8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000232451	ENST00000440785.1	n.248+7029T>C		intron_variant	Intron 1 of 3	3
ENSG00000232451	ENST00000669447.1	n.121+7029T>C		intron_variant	Intron 1 of 4
ENSG00000232451	ENST00000791349.1	n.278+7029T>C		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.261 AC: 39627 AN: 152028 Hom.: 5535 Cov.: 32

Gnomad AFR AF: 0.202

Gnomad AMI AF: 0.183

Gnomad AMR AF: 0.204

Gnomad ASJ AF: 0.177

Gnomad EAS AF: 0.0963

Gnomad SAS AF: 0.272

Gnomad FIN AF: 0.329

Gnomad MID AF: 0.120

Gnomad NFE AF: 0.317

Gnomad OTH AF: 0.233

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

GnomAD4 genome AF: 0.261 AC: 39651 AN: 152146 Hom.: 5533 Cov.: 32 AF XY: 0.258 AC XY: 19183 AN XY: 74380

African (AFR) AF: 0.202 AC: 8384 AN: 41520

American (AMR) AF: 0.203 AC: 3107 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.177 AC: 613 AN: 3466

East Asian (EAS) AF: 0.0960 AC: 497 AN: 5178

South Asian (SAS) AF: 0.270 AC: 1301 AN: 4812

European-Finnish (FIN) AF: 0.329 AC: 3474 AN: 10572

Middle Eastern (MID) AF: 0.136 AC: 40 AN: 294

European-Non Finnish (NFE) AF: 0.317 AC: 21571 AN: 67984

Other (OTH) AF: 0.235 AC: 497 AN: 2116

Alfa AF: 0.290 Hom.: 25331

Bravo AF: 0.246

Asia WGS AF: 0.218 AC: 758 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	4.0
DANN	Benign	0.76
PhyloP100		0.055

Splicing

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

Other links and lift over

dbSNP: rs1449984; hg19: chr2-23414651;