rs1677

chr2-241227135-G-Achr2-241227135-G-C

Variant summary

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

The XR_001739176.3(LOC105376810):n.333G>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 0.733 in 152,264 control chromosomes in the GnomAD database, including 42,097 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 0.73 (42042 hom., cov: 31)
  • Exomes 𝑓: 0.84 (55 hom.)
• Consequence: LOC105376810 XR_001739176.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -4.09

Genes affected

LOC105376810 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.927 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105376810	XR_001739176.3	n.333G>A		non_coding_transcript_exon_variant	2/2
ANO7	XM_011511267.3	c.2444+8754G>A		intron_variant
ANO7	XM_017004229.2	c.2298+8754G>A		intron_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.732 AC: 111316 AN: 151988 Hom.: 42007 Cov.: 31

Gnomad AFR AF: 0.540

Gnomad AMI AF: 0.845

Gnomad AMR AF: 0.832

Gnomad ASJ AF: 0.840

Gnomad EAS AF: 0.949

Gnomad SAS AF: 0.706

Gnomad FIN AF: 0.829

Gnomad MID AF: 0.835

Gnomad NFE AF: 0.788

Gnomad OTH AF: 0.780

GnomAD4 exome AF: 0.835 AC: 132 AN: 158 Hom.: 55 AF XY: 0.854 AC XY: 82 AN XY: 96

Gnomad4 AMR exome AF: 1.00

Gnomad4 ASJ exome AF: 0.500

Gnomad4 FIN exome AF: 0.856

Gnomad4 NFE exome AF: 0.793

Gnomad4 OTH exome AF: 1.00

GnomAD4 genome AF: 0.732 AC: 111403 AN: 152106 Hom.: 42042 Cov.: 31 AF XY: 0.740 AC XY: 54993 AN XY: 74356

Gnomad4 AFR AF: 0.540

Gnomad4 AMR AF: 0.832

Gnomad4 ASJ AF: 0.840

Gnomad4 EAS AF: 0.949

Gnomad4 SAS AF: 0.707

Gnomad4 FIN AF: 0.829

Gnomad4 NFE AF: 0.788

Gnomad4 OTH AF: 0.783

Alfa AF: 0.790 Hom.: 45900

Bravo AF: 0.729

Asia WGS AF: 0.828 AC: 2879 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	0.026
Dann	Benign	0.30

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1677; hg19: chr2-242166550;