rs3916972

Positions:

• chr13-105594285-A-C
• chr13-105594285-A-G
• chr13-105594285-A-T

Variant summary

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

The XR_931698.2(LOC105370345):​n.731-20938T>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 0.522 in 151,882 control chromosomes in the GnomAD database, including 23,895 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 0.52 (23895 hom., cov: 30)
• Consequence: LOC105370345 XR_931698.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.624

Genes affected

LOC105370345 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.756 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105370345	XR_931698.2	n.731-20938T>G		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.522 AC: 79245 AN: 151764 Hom.: 23887 Cov.: 30

Gnomad AFR AF: 0.200

Gnomad AMI AF: 0.688

Gnomad AMR AF: 0.696

Gnomad ASJ AF: 0.611

Gnomad EAS AF: 0.777

Gnomad SAS AF: 0.510

Gnomad FIN AF: 0.705

Gnomad MID AF: 0.535

Gnomad NFE AF: 0.625

Gnomad OTH AF: 0.558

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

GnomAD4 genome AF: 0.522 AC: 79270 AN: 151882 Hom.: 23895 Cov.: 30 AF XY: 0.532 AC XY: 39499 AN XY: 74220

Gnomad4 AFR AF: 0.199

Gnomad4 AMR AF: 0.697

Gnomad4 ASJ AF: 0.611

Gnomad4 EAS AF: 0.776

Gnomad4 SAS AF: 0.511

Gnomad4 FIN AF: 0.705

Gnomad4 NFE AF: 0.625

Gnomad4 OTH AF: 0.558

Alfa AF: 0.615 Hom.: 58209

Bravo AF: 0.513

Asia WGS AF: 0.628 AC: 2179 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.77
DANN	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3916972; hg19: chr13-106246634;