rs978797

Variant names:

• chr12-41878740-G-A
• rs978797
• ENST00000550874.1:n.472-48815C>T

Your query was ambiguous. Multiple possible variants found:

• chr12-41878740-G-A
• chr12-41878740-G-C
• chr12-41878740-G-T

Variant summary

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

The ENST00000550874.1(ENSG00000257239):​n.472-48815C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.529 in 151,922 control chromosomes in the GnomAD database, including 22,030 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 0.53 (22030 hom., cov: 32)
• Consequence: ENSG00000257239 ENST00000550874.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.207
• Publications: 2 publications found

Genes affected

ENSG00000257239 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.589 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
ENSG00000257239	ENST00000550874.1	n.472-48815C>T		intron_variant	Intron 1 of 1	3
ENSG00000257239	ENST00000824751.1	n.123-48815C>T		intron_variant	Intron 1 of 1
ENSG00000257239	ENST00000824752.1	n.244-16577C>T		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.529 AC: 80337 AN: 151804 Hom.: 22026 Cov.: 32

Gnomad AFR AF: 0.451

Gnomad AMI AF: 0.588

Gnomad AMR AF: 0.528

Gnomad ASJ AF: 0.594

Gnomad EAS AF: 0.203

Gnomad SAS AF: 0.446

Gnomad FIN AF: 0.588

Gnomad MID AF: 0.570

Gnomad NFE AF: 0.594

Gnomad OTH AF: 0.553

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

GnomAD4 genome AF: 0.529 AC: 80385 AN: 151922 Hom.: 22030 Cov.: 32 AF XY: 0.523 AC XY: 38870 AN XY: 74262

African (AFR) AF: 0.450 AC: 18636 AN: 41394

American (AMR) AF: 0.529 AC: 8081 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.594 AC: 2062 AN: 3472

East Asian (EAS) AF: 0.202 AC: 1046 AN: 5172

South Asian (SAS) AF: 0.446 AC: 2144 AN: 4806

European-Finnish (FIN) AF: 0.588 AC: 6196 AN: 10546

Middle Eastern (MID) AF: 0.571 AC: 168 AN: 294

European-Non Finnish (NFE) AF: 0.594 AC: 40352 AN: 67940

Other (OTH) AF: 0.553 AC: 1168 AN: 2112

Alfa AF: 0.451 Hom.: 1705

Bravo AF: 0.523

Asia WGS AF: 0.385 AC: 1340 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	6.5
DANN	Benign	0.58
PhyloP100		0.21

Splicing

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

Other links and lift over

dbSNP: rs978797; hg19: chr12-42272542;