chr1-209091807-T-C

Position:

• chr1-209091807-T-C

Variant summary

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

The XR_001738442.2(LOC107985255):​n.495+40947A>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 0.187 in 152,070 control chromosomes in the GnomAD database, including 2,868 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 0.19 (2868 hom., cov: 32)
• Consequence: LOC107985255 XR_001738442.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.691

Genes affected

LOC107985255 (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 (AFR) allele frequency at 95% confidence interval = 0.256 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC107985255	XR_001738442.2	n.495+40947A>G		intron_variant, non_coding_transcript_variant
LOC107985255	XR_001738441.2	n.495+40947A>G		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.187 AC: 28389 AN: 151952 Hom.: 2865 Cov.: 32

Gnomad AFR AF: 0.260

Gnomad AMI AF: 0.137

Gnomad AMR AF: 0.146

Gnomad ASJ AF: 0.191

Gnomad EAS AF: 0.130

Gnomad SAS AF: 0.111

Gnomad FIN AF: 0.150

Gnomad MID AF: 0.161

Gnomad NFE AF: 0.168

Gnomad OTH AF: 0.176

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

GnomAD4 genome AF: 0.187 AC: 28416 AN: 152070 Hom.: 2868 Cov.: 32 AF XY: 0.183 AC XY: 13622 AN XY: 74356

Gnomad4 AFR AF: 0.260

Gnomad4 AMR AF: 0.146

Gnomad4 ASJ AF: 0.191

Gnomad4 EAS AF: 0.130

Gnomad4 SAS AF: 0.112

Gnomad4 FIN AF: 0.150

Gnomad4 NFE AF: 0.168

Gnomad4 OTH AF: 0.175

Alfa AF: 0.149 Hom.: 1019

Bravo AF: 0.190

Asia WGS AF: 0.137 AC: 473 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.2
DANN	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1330232; hg19: chr1-209265152;