rs12065953

Positions:

• chr1-55427766-C-T

Variant summary

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

The ENST00000643167.1(ENSG00000234810):​n.138+98341C>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 0.109 in 152,138 control chromosomes in the GnomAD database, including 1,794 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 0.11 (1794 hom., cov: 32)
• Consequence: ENST00000643167.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.50

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.282 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
	ENST00000643167.1	n.138+98341C>T		intron_variant, non_coding_transcript_variant
	ENST00000646341.1	n.158+66201C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.109 AC: 16502 AN: 152020 Hom.: 1788 Cov.: 32

Gnomad AFR AF: 0.287

Gnomad AMI AF: 0.0252

Gnomad AMR AF: 0.0519

Gnomad ASJ AF: 0.0649

Gnomad EAS AF: 0.0929

Gnomad SAS AF: 0.0434

Gnomad FIN AF: 0.0252

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.0363

Gnomad OTH AF: 0.0861

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

GnomAD4 genome AF: 0.109 AC: 16539 AN: 152138 Hom.: 1794 Cov.: 32 AF XY: 0.106 AC XY: 7863 AN XY: 74382

Gnomad4 AFR AF: 0.287

Gnomad4 AMR AF: 0.0518

Gnomad4 ASJ AF: 0.0649

Gnomad4 EAS AF: 0.0927

Gnomad4 SAS AF: 0.0437

Gnomad4 FIN AF: 0.0252

Gnomad4 NFE AF: 0.0363

Gnomad4 OTH AF: 0.0857

Alfa AF: 0.0483 Hom.: 258

Bravo AF: 0.117

Asia WGS AF: 0.0940 AC: 326 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.046
DANN	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12065953; hg19: chr1-55893439;