rs2937673

Positions:

• chr3-117513540-A-G

Variant summary

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

The XR_924361.3(LOC105374056):​n.30023+197A>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 0.398 in 151,986 control chromosomes in the GnomAD database, including 14,789 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 0.40 (14789 hom., cov: 31)
• Consequence: LOC105374056 XR_924361.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.27

Genes affected

LOC105374056 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.56 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105374056	XR_924361.3	n.30023+197A>G		intron_variant, non_coding_transcript_variant
LOC105374056	XR_007096021.1	n.30023+197A>G		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.398 AC: 60481 AN: 151870 Hom.: 14794 Cov.: 31

Gnomad AFR AF: 0.128

Gnomad AMI AF: 0.371

Gnomad AMR AF: 0.332

Gnomad ASJ AF: 0.517

Gnomad EAS AF: 0.226

Gnomad SAS AF: 0.449

Gnomad FIN AF: 0.498

Gnomad MID AF: 0.532

Gnomad NFE AF: 0.565

Gnomad OTH AF: 0.418

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

GnomAD4 genome AF: 0.398 AC: 60458 AN: 151986 Hom.: 14789 Cov.: 31 AF XY: 0.392 AC XY: 29137 AN XY: 74270

Gnomad4 AFR AF: 0.128

Gnomad4 AMR AF: 0.332

Gnomad4 ASJ AF: 0.517

Gnomad4 EAS AF: 0.225

Gnomad4 SAS AF: 0.449

Gnomad4 FIN AF: 0.498

Gnomad4 NFE AF: 0.565

Gnomad4 OTH AF: 0.413

Alfa AF: 0.498 Hom.: 5976

Bravo AF: 0.370

Asia WGS AF: 0.325 AC: 1134 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	11
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: rs2937673; hg19: chr3-117232387;