rs2770228

chr13-97548318-G-Achr13-97548318-G-Cchr13-97548318-G-T

Variant summary

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

The XR_001749969.1(LOC105370325):n.105-243G>A 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 0.906 in 152,202 control chromosomes in the GnomAD database, including 63,315 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 0.91 (63315 hom., cov: 31)
• Consequence: LOC105370325 XR_001749969.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.428

Genes affected

LOC105370325 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.977 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105370325	XR_001749969.1	n.105-243G>A		intron_variant, non_coding_transcript_variant
LOC105370324	XR_007063845.1	n.2615-967C>T		intron_variant, non_coding_transcript_variant
LOC105370324	XR_931663.3	n.2671-967C>T		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.906 AC: 137790 AN: 152084 Hom.: 63280 Cov.: 31

Gnomad AFR AF: 0.736

Gnomad AMI AF: 0.909

Gnomad AMR AF: 0.955

Gnomad ASJ AF: 0.969

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.966

Gnomad FIN AF: 0.990

Gnomad MID AF: 0.939

Gnomad NFE AF: 0.970

Gnomad OTH AF: 0.918

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

GnomAD4 genome AF: 0.906 AC: 137879 AN: 152202 Hom.: 63315 Cov.: 31 AF XY: 0.910 AC XY: 67711 AN XY: 74420

Gnomad4 AFR AF: 0.736

Gnomad4 AMR AF: 0.955

Gnomad4 ASJ AF: 0.969

Gnomad4 EAS AF: 0.999

Gnomad4 SAS AF: 0.966

Gnomad4 FIN AF: 0.990

Gnomad4 NFE AF: 0.970

Gnomad4 OTH AF: 0.919

Alfa AF: 0.928 Hom.: 9418

Bravo AF: 0.895

Asia WGS AF: 0.964 AC: 3351 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
Cadd	Benign	1.1
Dann	Benign	0.29

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2770228; hg19: chr13-98200572;