rs11705701

Variant names:

• chr3-185826521-G-A
• rs11705701
• ENST00000764831.1:n.63G>A

Your query was ambiguous. Multiple possible variants found:

• chr3-185826521-G-A
• chr3-185826521-G-C

Variant summary

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

The ENST00000764831.1(ENSG00000299582):​n.63G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.538 in 152,104 control chromosomes in the GnomAD database, including 24,350 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 0.54 (24350 hom., cov: 32)
• Consequence: ENSG00000299582 ENST00000764831.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.337
• Publications: 36 publications found

Genes affected

ENSG00000299582 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.804 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
ENSG00000299582	ENST00000764831.1	n.63G>A		non_coding_transcript_exon_variant	Exon 2 of 4
ENSG00000299582	ENST00000764832.1	n.186G>A		non_coding_transcript_exon_variant	Exon 2 of 4
ENSG00000299582	ENST00000764833.1	n.161G>A		non_coding_transcript_exon_variant	Exon 2 of 4

Frequencies

GnomAD3 genomes AF: 0.538 AC: 81762 AN: 151986 Hom.: 24296 Cov.: 32

Gnomad AFR AF: 0.811

Gnomad AMI AF: 0.688

Gnomad AMR AF: 0.400

Gnomad ASJ AF: 0.525

Gnomad EAS AF: 0.244

Gnomad SAS AF: 0.465

Gnomad FIN AF: 0.426

Gnomad MID AF: 0.506

Gnomad NFE AF: 0.447

Gnomad OTH AF: 0.512

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

GnomAD4 genome AF: 0.538 AC: 81882 AN: 152104 Hom.: 24350 Cov.: 32 AF XY: 0.532 AC XY: 39565 AN XY: 74356

African (AFR) AF: 0.812 AC: 33691 AN: 41508

American (AMR) AF: 0.400 AC: 6113 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.525 AC: 1819 AN: 3466

East Asian (EAS) AF: 0.244 AC: 1262 AN: 5178

South Asian (SAS) AF: 0.466 AC: 2246 AN: 4824

European-Finnish (FIN) AF: 0.426 AC: 4495 AN: 10556

Middle Eastern (MID) AF: 0.510 AC: 150 AN: 294

European-Non Finnish (NFE) AF: 0.447 AC: 30400 AN: 67960

Other (OTH) AF: 0.512 AC: 1080 AN: 2108

Alfa AF: 0.473 Hom.: 23579

Bravo AF: 0.542

Asia WGS AF: 0.434 AC: 1511 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	13
DANN	Benign	0.69
PhyloP100		0.34

Splicing

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

Other links and lift over

dbSNP: rs11705701; hg19: chr3-185544309;