rs2365403

Positions:

• chr17-67699983-C-G

Variant summary

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

The XR_002958126.2(LOC101928045):​n.229-10610G>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 0.19 in 151,970 control chromosomes in the GnomAD database, including 2,868 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 0.19 (2868 hom., cov: 31)
• Consequence: LOC101928045 XR_002958126.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.679

Genes affected

LOC101928045 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.256 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC101928045	XR_002958126.2	n.229-10610G>C		intron_variant, non_coding_transcript_variant
LOC101928045	XR_002958128.2	n.1696G>C		non_coding_transcript_exon_variant	1/3
LOC101928045	XR_002958125.2	n.186-10610G>C		intron_variant, non_coding_transcript_variant
LOC101928045	XR_002958127.2	n.38-10610G>C		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.190 AC: 28897 AN: 151852 Hom.: 2865 Cov.: 31

Gnomad AFR AF: 0.234

Gnomad AMI AF: 0.296

Gnomad AMR AF: 0.154

Gnomad ASJ AF: 0.0812

Gnomad EAS AF: 0.268

Gnomad SAS AF: 0.0890

Gnomad FIN AF: 0.229

Gnomad MID AF: 0.172

Gnomad NFE AF: 0.173

Gnomad OTH AF: 0.157

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

GnomAD4 genome AF: 0.190 AC: 28934 AN: 151970 Hom.: 2868 Cov.: 31 AF XY: 0.189 AC XY: 14060 AN XY: 74274

Gnomad4 AFR AF: 0.234

Gnomad4 AMR AF: 0.154

Gnomad4 ASJ AF: 0.0812

Gnomad4 EAS AF: 0.268

Gnomad4 SAS AF: 0.0895

Gnomad4 FIN AF: 0.229

Gnomad4 NFE AF: 0.173

Gnomad4 OTH AF: 0.158

Alfa AF: 0.177 Hom.: 329

Bravo AF: 0.189

Asia WGS AF: 0.165 AC: 571 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.63
DANN	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2365403; hg19: chr17-65696099;