rs2001114

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 10 publications found

Genes affected

ENSG00000272980 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000705249.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000272980	ENST00000705249.1		c.1065+39119A>G		intron	N/A	ENSP00000516101.1
	ENSG00000272980	ENST00000705250.1		c.843+39119A>G		intron	N/A	ENSP00000516102.1
	ENSG00000272980	ENST00000705254.1		c.672+39119A>G		intron	N/A	ENSP00000516106.1

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

African (AFR) AF: 0.185 AC: 7680 AN: 41484

American (AMR) AF: 0.320 AC: 4882 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.375 AC: 1301 AN: 3472

East Asian (EAS) AF: 0.376 AC: 1949 AN: 5180

South Asian (SAS) AF: 0.312 AC: 1503 AN: 4812

European-Finnish (FIN) AF: 0.385 AC: 4046 AN: 10510

Middle Eastern (MID) AF: 0.435 AC: 128 AN: 294

European-Non Finnish (NFE) AF: 0.415 AC: 28169 AN: 67922

Other (OTH) AF: 0.337 AC: 710 AN: 2108

Alfa AF: 0.359 Hom.: 3423

Bravo AF: 0.320

Asia WGS AF: 0.326 AC: 1135 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	12
DANN	Benign	0.82
PhyloP100		0.32

Splicing

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

Other links and lift over

dbSNP: rs2001114; hg19: chr6-167486578;