chr12-95999809-C-T

Variant names:

• chr12-95999809-C-T
• rs61937881
• ENST00000551849.2:n.172-282C>T

Variant summary

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

The ENST00000551849.2(ENSG00000257878):​n.172-282C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.167 in 152,196 control chromosomes in the GnomAD database, including 2,788 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 0.17 (2788 hom., cov: 32)
• Consequence: ENSG00000257878 ENST00000551849.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0280
• Publications: 10 publications found

Genes affected

ENSG00000257878 (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 (NFE) allele frequency at 95% confidence interval = 0.253 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC102723340	XR_001749275.3	n.150-282C>T		intron_variant	Intron 1 of 2
LOC102723340	XR_002957424.2	n.149+3179C>T		intron_variant	Intron 1 of 1
LOC102723340	XR_945236.4	n.571-282C>T		intron_variant	Intron 2 of 3
LOC102723340	XR_945237.4	n.247-282C>T		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000257878	ENST00000551849.2	n.172-282C>T		intron_variant	Intron 1 of 3	3
ENSG00000257878	ENST00000684881.3	n.176+3179C>T		intron_variant	Intron 1 of 2
ENSG00000257878	ENST00000689841.2	n.265-282C>T		intron_variant	Intron 2 of 4

Frequencies

GnomAD3 genomes AF: 0.167 AC: 25382 AN: 152078 Hom.: 2788 Cov.: 32

Gnomad AFR AF: 0.0491

Gnomad AMI AF: 0.210

Gnomad AMR AF: 0.148

Gnomad ASJ AF: 0.194

Gnomad EAS AF: 0.0185

Gnomad SAS AF: 0.114

Gnomad FIN AF: 0.165

Gnomad MID AF: 0.165

Gnomad NFE AF: 0.257

Gnomad OTH AF: 0.158

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

GnomAD4 genome AF: 0.167 AC: 25379 AN: 152196 Hom.: 2788 Cov.: 32 AF XY: 0.160 AC XY: 11938 AN XY: 74390

African (AFR) AF: 0.0489 AC: 2033 AN: 41540

American (AMR) AF: 0.148 AC: 2268 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.194 AC: 673 AN: 3470

East Asian (EAS) AF: 0.0185 AC: 96 AN: 5182

South Asian (SAS) AF: 0.115 AC: 555 AN: 4826

European-Finnish (FIN) AF: 0.165 AC: 1745 AN: 10594

Middle Eastern (MID) AF: 0.160 AC: 47 AN: 294

European-Non Finnish (NFE) AF: 0.257 AC: 17442 AN: 67978

Other (OTH) AF: 0.156 AC: 329 AN: 2114

Alfa AF: 0.195 Hom.: 407

Bravo AF: 0.161

Asia WGS AF: 0.0610 AC: 213 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.1
DANN	Benign	0.46
PhyloP100		-0.028

Splicing

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

Other links and lift over

dbSNP: rs61937881; hg19: chr12-96393587;