rs12029080

Positions:

• chr1-94587797-T-G

Variant summary

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

The ENST00000413541.1(ENSG00000223675):​n.965-1035A>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 0.242 in 152,060 control chromosomes in the GnomAD database, including 5,065 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 0.24 (5065 hom., cov: 32)
• Consequence: ENST00000413541.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.142

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.292 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105378861	XR_001738160.3	n.511+24184T>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000413541.1	n.965-1035A>C		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.242 AC: 36742 AN: 151942 Hom.: 5069 Cov.: 32

Gnomad AFR AF: 0.111

Gnomad AMI AF: 0.274

Gnomad AMR AF: 0.270

Gnomad ASJ AF: 0.431

Gnomad EAS AF: 0.258

Gnomad SAS AF: 0.246

Gnomad FIN AF: 0.292

Gnomad MID AF: 0.269

Gnomad NFE AF: 0.295

Gnomad OTH AF: 0.262

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

GnomAD4 genome AF: 0.242 AC: 36746 AN: 152060 Hom.: 5065 Cov.: 32 AF XY: 0.243 AC XY: 18068 AN XY: 74344

Gnomad4 AFR AF: 0.111

Gnomad4 AMR AF: 0.270

Gnomad4 ASJ AF: 0.431

Gnomad4 EAS AF: 0.258

Gnomad4 SAS AF: 0.246

Gnomad4 FIN AF: 0.292

Gnomad4 NFE AF: 0.295

Gnomad4 OTH AF: 0.259

Alfa AF: 0.293 Hom.: 11968

Bravo AF: 0.235

Asia WGS AF: 0.247 AC: 859 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	3.7
DANN	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12029080; hg19: chr1-95053353;