rs61937881

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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000551849.2. 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
	ENSG00000257878	ENST00000551849.2	TSL:3	n.172-282C>T		intron	N/A
	ENSG00000257878	ENST00000684881.3		n.176+3179C>T		intron	N/A
	ENSG00000257878	ENST00000689841.2		n.265-282C>T		intron	N/A

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 v4.9

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs61937881;

hg19: chr12-96393587;