rs2070996

Positions:

• chr5-172771497-G-A

Variant summary

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

The XR_941232.3(LOC105377730):​n.139G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.207 in 152,048 control chromosomes in the GnomAD database, including 3,729 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 0.21 (3729 hom., cov: 32)
• Consequence: LOC105377730 XR_941232.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.658

Genes affected

LOC105377730 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.66).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.377 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105377730	XR_941232.3	n.139G>A		non_coding_transcript_exon_variant	1/2
LOC105377730	XR_941233.3	n.139G>A		non_coding_transcript_exon_variant	1/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000523005.1	n.70-5995G>A		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.207 AC: 31408 AN: 151932 Hom.: 3720 Cov.: 32

Gnomad AFR AF: 0.112

Gnomad AMI AF: 0.219

Gnomad AMR AF: 0.266

Gnomad ASJ AF: 0.384

Gnomad EAS AF: 0.392

Gnomad SAS AF: 0.290

Gnomad FIN AF: 0.252

Gnomad MID AF: 0.256

Gnomad NFE AF: 0.214

Gnomad OTH AF: 0.231

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

GnomAD4 genome AF: 0.207 AC: 31428 AN: 152048 Hom.: 3729 Cov.: 32 AF XY: 0.210 AC XY: 15639 AN XY: 74338

Gnomad4 AFR AF: 0.112

Gnomad4 AMR AF: 0.266

Gnomad4 ASJ AF: 0.384

Gnomad4 EAS AF: 0.392

Gnomad4 SAS AF: 0.289

Gnomad4 FIN AF: 0.252

Gnomad4 NFE AF: 0.214

Gnomad4 OTH AF: 0.235

Alfa AF: 0.213 Hom.: 462

Bravo AF: 0.204

Asia WGS AF: 0.354 AC: 1231 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.66
CADD	Benign	6.8
DANN	Benign	0.96

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2070996; hg19: chr5-172198500; COSMIC: COSV53321260;