rs2000292

Variant names:

• chr6-77457228-G-A
• rs2000292
• XM_047419660.1:c.-3743+15795G>A

Your query was ambiguous. Multiple possible variants found:

• chr6-77457228-G-A
• chr6-77457228-G-C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000741460.1(ENSG00000296734):​n.48+9672C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.309 in 151,786 control chromosomes in the GnomAD database, including 7,534 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 0.31 (7534 hom., cov: 32)
• Consequence: ENSG00000296734 ENST00000741460.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.692
• Publications: 10 publications found

Genes affected

LOC105377864 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.451 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000741460.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000296734	ENST00000741460.1		n.48+9672C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.309 AC: 46814 AN: 151668 Hom.: 7529 Cov.: 32

Gnomad AFR AF: 0.378

Gnomad AMI AF: 0.323

Gnomad AMR AF: 0.349

Gnomad ASJ AF: 0.246

Gnomad EAS AF: 0.465

Gnomad SAS AF: 0.319

Gnomad FIN AF: 0.222

Gnomad MID AF: 0.316

Gnomad NFE AF: 0.262

Gnomad OTH AF: 0.309

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

GnomAD4 genome AF: 0.309 AC: 46838 AN: 151786 Hom.: 7534 Cov.: 32 AF XY: 0.309 AC XY: 22911 AN XY: 74176

African (AFR) AF: 0.377 AC: 15568 AN: 41294

American (AMR) AF: 0.349 AC: 5327 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.246 AC: 852 AN: 3468

East Asian (EAS) AF: 0.466 AC: 2401 AN: 5148

South Asian (SAS) AF: 0.319 AC: 1538 AN: 4820

European-Finnish (FIN) AF: 0.222 AC: 2344 AN: 10548

Middle Eastern (MID) AF: 0.316 AC: 93 AN: 294

European-Non Finnish (NFE) AF: 0.262 AC: 17771 AN: 67932

Other (OTH) AF: 0.309 AC: 651 AN: 2104

Alfa AF: 0.279 Hom.: 4024

Bravo AF: 0.321

Asia WGS AF: 0.364 AC: 1265 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.1
DANN	Benign	0.79
PhyloP100		-0.69

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs2000292;

hg19: chr6-78166945;