rs999297

Variant names:

• chr11-61033838-C-A
• rs999297
• ENST00000794255.1:n.136-20298G>T

Your query was ambiguous. Multiple possible variants found:

• chr11-61033838-C-A
• chr11-61033838-C-G
• chr11-61033838-C-T

Variant summary

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

The ENST00000794255.1(ENSG00000303405):​n.136-20298G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.268 in 152,064 control chromosomes in the GnomAD database, including 7,170 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 0.27 (7170 hom., cov: 32)
• Consequence: ENSG00000303405 ENST00000794255.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.927
• Publications: 10 publications found

Genes affected

ENSG00000303405 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.535 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105369325	NR_188502.1	n.63-3443G>T		intron_variant	Intron 1 of 1
LOC105369325	NR_188503.1	n.274-3443G>T		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000303405	ENST00000794255.1	n.136-20298G>T		intron_variant	Intron 1 of 1
ENSG00000303405	ENST00000794256.1	n.229-20298G>T		intron_variant	Intron 2 of 2
ENSG00000303405	ENST00000794257.1	n.349+9228G>T		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.268 AC: 40671 AN: 151946 Hom.: 7159 Cov.: 32

Gnomad AFR AF: 0.0623

Gnomad AMI AF: 0.130

Gnomad AMR AF: 0.418

Gnomad ASJ AF: 0.190

Gnomad EAS AF: 0.551

Gnomad SAS AF: 0.421

Gnomad FIN AF: 0.458

Gnomad MID AF: 0.134

Gnomad NFE AF: 0.304

Gnomad OTH AF: 0.247

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

GnomAD4 genome AF: 0.268 AC: 40686 AN: 152064 Hom.: 7170 Cov.: 32 AF XY: 0.281 AC XY: 20901 AN XY: 74324

African (AFR) AF: 0.0622 AC: 2580 AN: 41510

American (AMR) AF: 0.420 AC: 6412 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.190 AC: 660 AN: 3470

East Asian (EAS) AF: 0.552 AC: 2851 AN: 5168

South Asian (SAS) AF: 0.420 AC: 2023 AN: 4818

European-Finnish (FIN) AF: 0.458 AC: 4831 AN: 10558

Middle Eastern (MID) AF: 0.120 AC: 35 AN: 292

European-Non Finnish (NFE) AF: 0.304 AC: 20651 AN: 67942

Other (OTH) AF: 0.248 AC: 524 AN: 2110

Alfa AF: 0.277 Hom.: 19136

Bravo AF: 0.253

Asia WGS AF: 0.460 AC: 1599 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	8.4
DANN	Benign	0.82
PhyloP100		0.93

Splicing

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

Other links and lift over

dbSNP: rs999297; hg19: chr11-60801310;