rs2001114

Variant names:

• chr6-167073090-A-G
• rs2001114
• ENST00000705249.1:c.1065+39119A>G

Variant summary

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

The ENST00000705249.1(ENSG00000272980):​c.1065+39119A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.333 in 151,962 control chromosomes in the GnomAD database, including 9,122 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 0.33 (9122 hom., cov: 32)
• Consequence: ENSG00000272980 ENST00000705249.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.322

Genes affected

ENSG00000272980 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.411 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000272980	ENST00000705249.1	c.1065+39119A>G		intron_variant	Intron 11 of 12			ENSP00000516101.1

Frequencies

GnomAD3 genomes AF: 0.333 AC: 50534 AN: 151844 Hom.: 9126 Cov.: 32

Gnomad AFR AF: 0.185

Gnomad AMI AF: 0.185

Gnomad AMR AF: 0.320

Gnomad ASJ AF: 0.375

Gnomad EAS AF: 0.376

Gnomad SAS AF: 0.314

Gnomad FIN AF: 0.385

Gnomad MID AF: 0.430

Gnomad NFE AF: 0.415

Gnomad OTH AF: 0.339

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

GnomAD4 genome AF: 0.333 AC: 50536 AN: 151962 Hom.: 9122 Cov.: 32 AF XY: 0.332 AC XY: 24688 AN XY: 74282

Gnomad4 AFR AF: 0.185

Gnomad4 AMR AF: 0.320

Gnomad4 ASJ AF: 0.375

Gnomad4 EAS AF: 0.376

Gnomad4 SAS AF: 0.312

Gnomad4 FIN AF: 0.385

Gnomad4 NFE AF: 0.415

Gnomad4 OTH AF: 0.337

Alfa AF: 0.350 Hom.: 1607

Bravo AF: 0.320

Asia WGS AF: 0.326 AC: 1135 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	12
DANN	Benign	0.82

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2001114; hg19: chr6-167486578;