rs4128918

Positions:

• chr5-71922769-G-A
• chr5-71922769-G-C

Variant summary

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

The XR_001742515.2(LOC107986382):​n.213+332C>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 0.128 in 151,992 control chromosomes in the GnomAD database, including 2,282 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 0.13 (2282 hom., cov: 32)
• Consequence: LOC107986382 XR_001742515.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.267

Genes affected

LOC107986382 (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 (AFR) allele frequency at 95% confidence interval = 0.308 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC107986382	XR_001742515.2	n.213+332C>T		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.127 AC: 19337 AN: 151874 Hom.: 2266 Cov.: 32

Gnomad AFR AF: 0.312

Gnomad AMI AF: 0.219

Gnomad AMR AF: 0.0745

Gnomad ASJ AF: 0.0931

Gnomad EAS AF: 0.0671

Gnomad SAS AF: 0.0388

Gnomad FIN AF: 0.0333

Gnomad MID AF: 0.0949

Gnomad NFE AF: 0.0539

Gnomad OTH AF: 0.104

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

GnomAD4 genome AF: 0.128 AC: 19385 AN: 151992 Hom.: 2282 Cov.: 32 AF XY: 0.124 AC XY: 9209 AN XY: 74298

Gnomad4 AFR AF: 0.312

Gnomad4 AMR AF: 0.0744

Gnomad4 ASJ AF: 0.0931

Gnomad4 EAS AF: 0.0666

Gnomad4 SAS AF: 0.0389

Gnomad4 FIN AF: 0.0333

Gnomad4 NFE AF: 0.0539

Gnomad4 OTH AF: 0.103

Alfa AF: 0.0508 Hom.: 95

Bravo AF: 0.139

Asia WGS AF: 0.0700 AC: 246 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	5.5
DANN	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4128918; hg19: chr5-71218596;