rs2030891

Positions:

• chr5-61752940-T-A
• chr5-61752940-T-C

Variant summary

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

The ENST00000667197.1(C5orf64):​n.700+2396T>A 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 0.746 in 152,176 control chromosomes in the GnomAD database, including 43,142 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 0.75 (43142 hom., cov: 32)
• Consequence: C5orf64 ENST00000667197.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.72

Genes affected

C5orf64 (HGNC:26744): (long intergenic non-protein coding RNA 3122) Predicted to be located in extracellular region. [provided by Alliance of Genome Resources, Apr 2022]

LOC124900983 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.874 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124900983	XR_007058783.1	n.408+2396T>A		intron_variant, non_coding_transcript_variant
LOC124900983	XR_007058782.1	n.301+1170T>A		intron_variant, non_coding_transcript_variant
LOC124900983	XR_007058784.1	n.201-2892T>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
C5orf64	ENST00000667197.1	n.700+2396T>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.746 AC: 113382 AN: 152058 Hom.: 43107 Cov.: 32

Gnomad AFR AF: 0.882

Gnomad AMI AF: 0.724

Gnomad AMR AF: 0.631

Gnomad ASJ AF: 0.780

Gnomad EAS AF: 0.435

Gnomad SAS AF: 0.679

Gnomad FIN AF: 0.706

Gnomad MID AF: 0.791

Gnomad NFE AF: 0.721

Gnomad OTH AF: 0.756

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

GnomAD4 genome AF: 0.746 AC: 113470 AN: 152176 Hom.: 43142 Cov.: 32 AF XY: 0.739 AC XY: 54934 AN XY: 74376

Gnomad4 AFR AF: 0.882

Gnomad4 AMR AF: 0.630

Gnomad4 ASJ AF: 0.780

Gnomad4 EAS AF: 0.435

Gnomad4 SAS AF: 0.679

Gnomad4 FIN AF: 0.706

Gnomad4 NFE AF: 0.721

Gnomad4 OTH AF: 0.750

Alfa AF: 0.735 Hom.: 5177

Bravo AF: 0.743

Asia WGS AF: 0.579 AC: 2016 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.034
DANN	Benign	0.33

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2030891; hg19: chr5-61048767;