chr5-57658989-G-C

Position:

• chr5-57658989-G-C

Variant summary

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

The NR_104668.1(LOC101928505):​n.101-6262G>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 0.344 in 151,896 control chromosomes in the GnomAD database, including 11,779 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 0.34 (11779 hom., cov: 32)
• Consequence: LOC101928505 NR_104668.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.14

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.69).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.639 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC101928505	NR_104668.1	n.101-6262G>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000701975.1	n.227-6262G>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.344 AC: 52160 AN: 151778 Hom.: 11736 Cov.: 32

Gnomad AFR AF: 0.645

Gnomad AMI AF: 0.148

Gnomad AMR AF: 0.269

Gnomad ASJ AF: 0.210

Gnomad EAS AF: 0.311

Gnomad SAS AF: 0.152

Gnomad FIN AF: 0.258

Gnomad MID AF: 0.229

Gnomad NFE AF: 0.217

Gnomad OTH AF: 0.335

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

GnomAD4 genome AF: 0.344 AC: 52270 AN: 151896 Hom.: 11779 Cov.: 32 AF XY: 0.340 AC XY: 25283 AN XY: 74256

Gnomad4 AFR AF: 0.645

Gnomad4 AMR AF: 0.269

Gnomad4 ASJ AF: 0.210

Gnomad4 EAS AF: 0.311

Gnomad4 SAS AF: 0.153

Gnomad4 FIN AF: 0.258

Gnomad4 NFE AF: 0.217

Gnomad4 OTH AF: 0.334

Alfa AF: 0.276 Hom.: 894

Bravo AF: 0.361

Asia WGS AF: 0.297 AC: 1032 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.69
CADD	Benign	6.6
DANN	Benign	0.84

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs230827; hg19: chr5-56954816;