rs61937881

Positions:

• chr12-95999809-C-T

Variant summary

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

The ENST00000551849.2(ENSG00000257878):​n.172-282C>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 0.167 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: ENST00000551849.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0280

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

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC102723340	XR_945236.4	n.571-282C>T		intron_variant, non_coding_transcript_variant
LOC102723340	XR_001749275.3	n.150-282C>T		intron_variant, non_coding_transcript_variant
LOC102723340	XR_002957424.2	n.149+3179C>T		intron_variant, non_coding_transcript_variant
LOC102723340	XR_945237.4	n.247-282C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000551849.2	n.172-282C>T		intron_variant, non_coding_transcript_variant		3
	ENST00000684881.2	n.154+3179C>T		intron_variant, non_coding_transcript_variant
	ENST00000689841.1	n.265-282C>T		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.0489

Gnomad4 AMR AF: 0.148

Gnomad4 ASJ AF: 0.194

Gnomad4 EAS AF: 0.0185

Gnomad4 SAS AF: 0.115

Gnomad4 FIN AF: 0.165

Gnomad4 NFE AF: 0.257

Gnomad4 OTH AF: 0.156

Alfa AF: 0.200 Hom.: 405

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs61937881; hg19: chr12-96393587;