rs768763

Positions:

• chr5-41293268-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_007058748.1(LOC102723740):​n.116+1381T>C variant causes a intron, non coding transcript 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: LOC102723740 XR_007058748.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.11

Genes affected

LOC102723740 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
LOC102723740	XR_007058748.1	n.116+1381T>C		intron_variant, non_coding_transcript_variant
LOC124900969	XR_007058749.1	n.64-4432A>G		intron_variant, non_coding_transcript_variant
LOC102723740	XR_925953.3	n.247+549T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

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

Gnomad4 AFR AF: 0.0490

Gnomad4 AMR AF: 0.144

Gnomad4 ASJ AF: 0.164

Gnomad4 EAS AF: 0.231

Gnomad4 SAS AF: 0.200

Gnomad4 FIN AF: 0.183

Gnomad4 NFE AF: 0.187

Gnomad4 OTH AF: 0.164

Alfa AF: 0.178 Hom.: 3636

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs768763; hg19: chr5-41293370;