rs10491996

Variant names:

• chr12-41862995-G-A
• rs10491996
• ENST00000550874.1:n.472-33070C>T

Your query was ambiguous. Multiple possible variants found:

• chr12-41862995-G-A
• chr12-41862995-G-C
• chr12-41862995-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000550874.1(ENSG00000257239):​n.472-33070C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.927 in 152,288 control chromosomes in the GnomAD database, including 65,504 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 0.93 (65504 hom., cov: 33)
• Consequence: ENSG00000257239 ENST00000550874.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.325

Genes affected

ENSG00000257239 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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 = 0.977 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.472-33070C>T		intron_variant	Intron 1 of 1	3

Frequencies

GnomAD3 genomes AF: 0.927 AC: 141017 AN: 152170 Hom.: 65459 Cov.: 33

Gnomad AFR AF: 0.870

Gnomad AMI AF: 0.963

Gnomad AMR AF: 0.943

Gnomad ASJ AF: 0.940

Gnomad EAS AF: 1.00

Gnomad SAS AF: 0.981

Gnomad FIN AF: 0.968

Gnomad MID AF: 0.949

Gnomad NFE AF: 0.940

Gnomad OTH AF: 0.926

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

GnomAD4 genome AF: 0.927 AC: 141117 AN: 152288 Hom.: 65504 Cov.: 33 AF XY: 0.930 AC XY: 69225 AN XY: 74468

Gnomad4 AFR AF: 0.870

Gnomad4 AMR AF: 0.943

Gnomad4 ASJ AF: 0.940

Gnomad4 EAS AF: 1.00

Gnomad4 SAS AF: 0.981

Gnomad4 FIN AF: 0.968

Gnomad4 NFE AF: 0.940

Gnomad4 OTH AF: 0.927

Alfa AF: 0.938 Hom.: 86473

Bravo AF: 0.922

Asia WGS AF: 0.977 AC: 3398 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.8
DANN	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10491996; hg19: chr12-42256797;