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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC102723740	XR_007058748.1	n.116+1381T>C		intron_variant	Intron 1 of 1
LOC124900969	XR_007058749.1	n.64-4432A>G		intron_variant	Intron 1 of 2
LOC102723740	XR_925953.3	n.247+549T>C		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000300694	ENST00000773507.1	n.223T>C		non_coding_transcript_exon_variant	Exon 1 of 2
ENSG00000300694	ENST00000773508.1	n.213T>C		non_coding_transcript_exon_variant	Exon 1 of 2
ENSG00000300694	ENST00000773503.1	n.276+1381T>C		intron_variant	Intron 1 of 1
ENSG00000300694	ENST00000773506.1	n.1220+408T>C		intron_variant	Intron 1 of 1

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 v4.3

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

Other links and lift over

dbSNP: rs768763; hg19: chr5-41293370;