rs2000292

Variant names:

• chr6-77457228-G-A
• rs2000292
• ENST00000741460.1:n.48+9672C>T

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

ENSG00000296734 (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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105377864	XM_047419660.1	c.-3743+15795G>A		intron_variant	Intron 5 of 8		XP_047275616.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000296734	ENST00000741460.1	n.48+9672C>T		intron_variant	Intron 1 of 3

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 v4.3

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

Other links and lift over

dbSNP: rs2000292; hg19: chr6-78166945;