rs10491996

chr12-41862995-G-Achr12-41862995-G-Cchr12-41862995-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, non coding transcript 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: ENST00000550874.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.325

Genes affected

(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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000550874.1	n.472-33070C>T		intron_variant, non_coding_transcript_variant		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;