rs410850

Positions:

• chr5-61675951-G-A
• chr5-61675951-G-T

Variant summary

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

The NR_109910.1(LOC101928651):​n.1161+1672C>T 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 0.357 in 152,004 control chromosomes in the GnomAD database, including 9,812 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 0.36 (9812 hom., cov: 32)
• Consequence: LOC101928651 NR_109910.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.92

Genes affected

(HGNC:):

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.381 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC101928651	NR_109910.1	n.1161+1672C>T		intron_variant, non_coding_transcript_variant
C5orf64	NR_161251.1	n.162-10932G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000513386.1	n.1161+1672C>T		intron_variant, non_coding_transcript_variant		1
C5orf64	ENST00000667197.1	n.156-27915G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.357 AC: 54166 AN: 151886 Hom.: 9807 Cov.: 32

Gnomad AFR AF: 0.386

Gnomad AMI AF: 0.194

Gnomad AMR AF: 0.288

Gnomad ASJ AF: 0.315

Gnomad EAS AF: 0.318

Gnomad SAS AF: 0.297

Gnomad FIN AF: 0.422

Gnomad MID AF: 0.212

Gnomad NFE AF: 0.357

Gnomad OTH AF: 0.341

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

GnomAD4 genome AF: 0.357 AC: 54206 AN: 152004 Hom.: 9812 Cov.: 32 AF XY: 0.359 AC XY: 26648 AN XY: 74272

Gnomad4 AFR AF: 0.386

Gnomad4 AMR AF: 0.287

Gnomad4 ASJ AF: 0.315

Gnomad4 EAS AF: 0.319

Gnomad4 SAS AF: 0.296

Gnomad4 FIN AF: 0.422

Gnomad4 NFE AF: 0.357

Gnomad4 OTH AF: 0.340

Alfa AF: 0.340 Hom.: 11747

Bravo AF: 0.344

Asia WGS AF: 0.364 AC: 1267 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.0070
DANN	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs410850; hg19: chr5-60971778;