rs77569097

Variant names:

• chr18-74292289-A-C
• rs77569097
• ENST00000660707.2:n.44A>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The ENST00000660707.2(ENSG00000286529):​n.44A>C 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 0.0145 in 152,294 control chromosomes in the GnomAD database, including 29 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 0.015 (29 hom., cov: 32)
• Consequence: ENSG00000286529 ENST00000660707.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.935
• Publications: 0 publications found

Genes affected

ENSG00000286529 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BS1: Variant frequency is greater than expected in population sas. GnomAd4 allele frequency = 0.0145 (2212/152294) while in subpopulation SAS AF = 0.0442 (213/4824). AF 95% confidence interval is 0.0393. There are 29 homozygotes in GnomAd4. There are 1108 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 29 gene

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
ENSG00000286529	ENST00000660707.2	n.44A>C		non_coding_transcript_exon_variant	Exon 1 of 2
ENSG00000286529	ENST00000849951.1	n.77A>C		non_coding_transcript_exon_variant	Exon 1 of 3
ENSG00000286529	ENST00000849952.1	n.70A>C		non_coding_transcript_exon_variant	Exon 1 of 2

Frequencies

GnomAD3 genomes AF: 0.0145 AC: 2199 AN: 152176 Hom.: 29 Cov.: 32

Gnomad AFR AF: 0.0338

Gnomad AMI AF: 0.0121

Gnomad AMR AF: 0.00759

Gnomad ASJ AF: 0.00922

Gnomad EAS AF: 0.00289

Gnomad SAS AF: 0.0435

Gnomad FIN AF: 0.000377

Gnomad MID AF: 0.00949

Gnomad NFE AF: 0.00544

Gnomad OTH AF: 0.0167

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

GnomAD4 genome AF: 0.0145 AC: 2212 AN: 152294 Hom.: 29 Cov.: 32 AF XY: 0.0149 AC XY: 1108 AN XY: 74480

African (AFR) AF: 0.0340 AC: 1412 AN: 41576

American (AMR) AF: 0.00758 AC: 116 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.00922 AC: 32 AN: 3470

East Asian (EAS) AF: 0.00290 AC: 15 AN: 5174

South Asian (SAS) AF: 0.0442 AC: 213 AN: 4824

European-Finnish (FIN) AF: 0.000377 AC: 4 AN: 10610

Middle Eastern (MID) AF: 0.0102 AC: 3 AN: 294

European-Non Finnish (NFE) AF: 0.00545 AC: 371 AN: 68016

Other (OTH) AF: 0.0166 AC: 35 AN: 2114

Alfa AF: 0.0126 Hom.: 1

Bravo AF: 0.0149

Asia WGS AF: 0.0310 AC: 109 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	1.9
DANN	Benign	0.35
PhyloP100		-0.94
PromoterAI		0.083	Neutral

Splicing

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

Other links and lift over

dbSNP: rs77569097; hg19: chr18-71959524;