11-65815595-G-T

Variant names:

• chr11-65815595-G-T
• rs3903072
• ENST00000790847.1:n.134C>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

ENSG00000302979 (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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124902693	XM_047427980.1	c.*1057+8928C>A		intron_variant	Intron 3 of 6		XP_047283936.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000302979	ENST00000790847.1	n.134C>A		non_coding_transcript_exon_variant	Exon 2 of 2
ENSG00000303001	ENST00000790959.1	n.340+199G>T		intron_variant	Intron 1 of 1

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 v4.3

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

Other links and lift over

dbSNP: rs3903072; hg19: chr11-65583066;