rs12634193

Positions:

• chr3-171462896-T-C

Variant summary

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

The ENST00000657847.1(ENSG00000240497):​n.144+3505T>C 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 0.773 in 152,136 control chromosomes in the GnomAD database, including 45,632 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 0.77 (45632 hom., cov: 33)
• Consequence: ENST00000657847.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.41

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 (AFR) allele frequency at 95% confidence interval = 0.835 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC102724479	XR_001740531.3	n.458+1539T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000657847.1	n.144+3505T>C		intron_variant, non_coding_transcript_variant
	ENST00000665680.1	n.84+2604T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.773 AC: 117554 AN: 152018 Hom.: 45585 Cov.: 33

Gnomad AFR AF: 0.842

Gnomad AMI AF: 0.669

Gnomad AMR AF: 0.746

Gnomad ASJ AF: 0.796

Gnomad EAS AF: 0.758

Gnomad SAS AF: 0.711

Gnomad FIN AF: 0.753

Gnomad MID AF: 0.756

Gnomad NFE AF: 0.747

Gnomad OTH AF: 0.769

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

GnomAD4 genome AF: 0.773 AC: 117664 AN: 152136 Hom.: 45632 Cov.: 33 AF XY: 0.771 AC XY: 57377 AN XY: 74394

Gnomad4 AFR AF: 0.842

Gnomad4 AMR AF: 0.746

Gnomad4 ASJ AF: 0.796

Gnomad4 EAS AF: 0.758

Gnomad4 SAS AF: 0.712

Gnomad4 FIN AF: 0.753

Gnomad4 NFE AF: 0.747

Gnomad4 OTH AF: 0.769

Alfa AF: 0.750 Hom.: 55699

Bravo AF: 0.780

Asia WGS AF: 0.748 AC: 2599 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	0.067
DANN	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12634193; hg19: chr3-171180685;