12-41862995-G-A

Variant names:

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

Variant summary

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

The ENST00000550874.1(ENSG00000257239):​n.472-33070C>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
• Publications: 1 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=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.977 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000550874.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000257239	ENST00000550874.1	TSL:3	n.472-33070C>T		intron	N/A
	ENSG00000257239	ENST00000824751.1		n.123-33070C>T		intron	N/A
	ENSG00000257239	ENST00000824752.1		n.244-832C>T		intron	N/A

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

African (AFR) AF: 0.870 AC: 36147 AN: 41534

American (AMR) AF: 0.943 AC: 14419 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.940 AC: 3261 AN: 3470

East Asian (EAS) AF: 1.00 AC: 5182 AN: 5182

South Asian (SAS) AF: 0.981 AC: 4741 AN: 4832

European-Finnish (FIN) AF: 0.968 AC: 10281 AN: 10620

Middle Eastern (MID) AF: 0.949 AC: 279 AN: 294

European-Non Finnish (NFE) AF: 0.940 AC: 63968 AN: 68036

Other (OTH) AF: 0.927 AC: 1961 AN: 2116

Alfa AF: 0.935 Hom.: 108498

Bravo AF: 0.922

Asia WGS AF: 0.977 AC: 3398 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.8
DANN	Benign	0.48
PhyloP100		-0.33

Splicing

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

Other links and lift over

dbSNP: rs10491996; hg19: chr12-42256797;