rs12741948

Positions:

• chr1-65709181-C-T

Variant summary

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

The ENST00000646875.1(ENSG00000285079):​n.346-1632C>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 0.261 in 152,030 control chromosomes in the GnomAD database, including 5,556 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 0.26 (5556 hom., cov: 31)
• Consequence: ENST00000646875.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.149

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.309 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000646875.1	n.346-1632C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.261 AC: 39655 AN: 151912 Hom.: 5556 Cov.: 31

Gnomad AFR AF: 0.205

Gnomad AMI AF: 0.361

Gnomad AMR AF: 0.275

Gnomad ASJ AF: 0.266

Gnomad EAS AF: 0.0237

Gnomad SAS AF: 0.233

Gnomad FIN AF: 0.247

Gnomad MID AF: 0.278

Gnomad NFE AF: 0.312

Gnomad OTH AF: 0.272

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

GnomAD4 genome AF: 0.261 AC: 39670 AN: 152030 Hom.: 5556 Cov.: 31 AF XY: 0.257 AC XY: 19099 AN XY: 74332

Gnomad4 AFR AF: 0.205

Gnomad4 AMR AF: 0.276

Gnomad4 ASJ AF: 0.266

Gnomad4 EAS AF: 0.0238

Gnomad4 SAS AF: 0.233

Gnomad4 FIN AF: 0.247

Gnomad4 NFE AF: 0.312

Gnomad4 OTH AF: 0.269

Alfa AF: 0.297 Hom.: 2702

Bravo AF: 0.261

Asia WGS AF: 0.110 AC: 384 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	5.3
DANN	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12741948; hg19: chr1-66174864;