rs768763

Variant names:

• chr5-41293268-A-G
• rs768763
• ENST00000773507.1:n.223T>C

Variant summary

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

The ENST00000773507.1(ENSG00000300694):​n.223T>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 0.146 in 152,174 control chromosomes in the GnomAD database, including 1,887 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 0.15 (1887 hom., cov: 31)
• Consequence: ENSG00000300694 ENST00000773507.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.11
• Publications: 8 publications found

Genes affected

ENSG00000300694 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.22 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000773507.1. 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
	ENSG00000300694	ENST00000773507.1		n.223T>C		non_coding_transcript_exon	Exon 1 of 2
	ENSG00000300694	ENST00000773508.1		n.213T>C		non_coding_transcript_exon	Exon 1 of 2
	ENSG00000300694	ENST00000773503.1		n.276+1381T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.146 AC: 22205 AN: 152054 Hom.: 1892 Cov.: 31

Gnomad AFR AF: 0.0490

Gnomad AMI AF: 0.193

Gnomad AMR AF: 0.145

Gnomad ASJ AF: 0.164

Gnomad EAS AF: 0.231

Gnomad SAS AF: 0.200

Gnomad FIN AF: 0.183

Gnomad MID AF: 0.256

Gnomad NFE AF: 0.187

Gnomad OTH AF: 0.166

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

GnomAD4 genome AF: 0.146 AC: 22195 AN: 152174 Hom.: 1887 Cov.: 31 AF XY: 0.147 AC XY: 10935 AN XY: 74390

African (AFR) AF: 0.0490 AC: 2037 AN: 41538

American (AMR) AF: 0.144 AC: 2208 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.164 AC: 570 AN: 3470

East Asian (EAS) AF: 0.231 AC: 1188 AN: 5146

South Asian (SAS) AF: 0.200 AC: 963 AN: 4824

European-Finnish (FIN) AF: 0.183 AC: 1938 AN: 10592

Middle Eastern (MID) AF: 0.252 AC: 74 AN: 294

European-Non Finnish (NFE) AF: 0.187 AC: 12694 AN: 67992

Other (OTH) AF: 0.164 AC: 347 AN: 2114

Alfa AF: 0.174 Hom.: 4744

Bravo AF: 0.139

Asia WGS AF: 0.203 AC: 709 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	7.3
DANN	Benign	0.62
PhyloP100		1.1

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: rs768763;

hg19: chr5-41293370;