11-65815595-G-T

Variant names:

• chr11-65815595-G-T
• rs3903072
• XM_047427980.1:c.*1057+8928C>A

Variant summary

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

The ENST00000790847.1(ENSG00000302979):​n.134C>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 0.372 in 152,028 control chromosomes in the GnomAD database, including 12,153 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 0.37 (12153 hom., cov: 32)
• Consequence: ENSG00000302979 ENST00000790847.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.808
• Publications: 92 publications found

Genes affected

LOC124902693 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.527 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000790847.1. 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
	ENSG00000302979	ENST00000790847.1		n.134C>A		non_coding_transcript_exon	Exon 2 of 2
	ENSG00000303001	ENST00000790959.1		n.340+199G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.372 AC: 56541 AN: 151910 Hom.: 12158 Cov.: 32

Gnomad AFR AF: 0.165

Gnomad AMI AF: 0.348

Gnomad AMR AF: 0.336

Gnomad ASJ AF: 0.463

Gnomad EAS AF: 0.207

Gnomad SAS AF: 0.545

Gnomad FIN AF: 0.550

Gnomad MID AF: 0.573

Gnomad NFE AF: 0.473

Gnomad OTH AF: 0.406

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

GnomAD4 genome AF: 0.372 AC: 56535 AN: 152028 Hom.: 12153 Cov.: 32 AF XY: 0.379 AC XY: 28140 AN XY: 74306

African (AFR) AF: 0.164 AC: 6812 AN: 41460

American (AMR) AF: 0.336 AC: 5135 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.463 AC: 1605 AN: 3470

East Asian (EAS) AF: 0.206 AC: 1066 AN: 5164

South Asian (SAS) AF: 0.545 AC: 2627 AN: 4824

European-Finnish (FIN) AF: 0.550 AC: 5809 AN: 10562

Middle Eastern (MID) AF: 0.561 AC: 165 AN: 294

European-Non Finnish (NFE) AF: 0.473 AC: 32138 AN: 67952

Other (OTH) AF: 0.408 AC: 861 AN: 2112

Alfa AF: 0.424 Hom.: 28151

Bravo AF: 0.340

Asia WGS AF: 0.376 AC: 1308 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	8.4
DANN	Benign	0.41
PhyloP100		0.81

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: rs3903072;

hg19: chr11-65583066;