rs4657039

chr1-161492938-A-G

Variant summary

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

The XR_922214.3(LOC105371473):n.1739-517A>G 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 0.509 in 151,904 control chromosomes in the GnomAD database, including 20,451 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 0.51 (20451 hom., cov: 31)
• Consequence: LOC105371473 XR_922214.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.320

Genes affected

LOC105371473 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.74).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.583 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105371473	XR_922214.3	n.1739-517A>G		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.509 AC: 77257 AN: 151786 Hom.: 20452 Cov.: 31

Gnomad AFR AF: 0.393

Gnomad AMI AF: 0.552

Gnomad AMR AF: 0.578

Gnomad ASJ AF: 0.505

Gnomad EAS AF: 0.247

Gnomad SAS AF: 0.416

Gnomad FIN AF: 0.519

Gnomad MID AF: 0.598

Gnomad NFE AF: 0.588

Gnomad OTH AF: 0.529

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

GnomAD4 genome AF: 0.509 AC: 77296 AN: 151904 Hom.: 20451 Cov.: 31 AF XY: 0.503 AC XY: 37355 AN XY: 74212

Gnomad4 AFR AF: 0.393

Gnomad4 AMR AF: 0.578

Gnomad4 ASJ AF: 0.505

Gnomad4 EAS AF: 0.247

Gnomad4 SAS AF: 0.416

Gnomad4 FIN AF: 0.519

Gnomad4 NFE AF: 0.588

Gnomad4 OTH AF: 0.528

Alfa AF: 0.565 Hom.: 49096

Bravo AF: 0.511

Asia WGS AF: 0.353 AC: 1232 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
Cadd	Benign	3.2
Dann	Benign	0.81

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4657039; hg19: chr1-161462728;