rs7571323

chr2-118074992-T-C

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The XR_001739662.3(LOC107985940):n.182-11976A>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 0.287 in 152,136 control chromosomes in the GnomAD database, including 6,644 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 0.29 (6644 hom., cov: 32)
• Consequence: LOC107985940 XR_001739662.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.16

Genes affected

LOC107985940 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.21).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.364 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC107985940	XR_001739662.3	n.182-11976A>G		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.287 AC: 43655 AN: 152018 Hom.: 6636 Cov.: 32

Gnomad AFR AF: 0.369

Gnomad AMI AF: 0.337

Gnomad AMR AF: 0.213

Gnomad ASJ AF: 0.296

Gnomad EAS AF: 0.138

Gnomad SAS AF: 0.276

Gnomad FIN AF: 0.192

Gnomad MID AF: 0.307

Gnomad NFE AF: 0.280

Gnomad OTH AF: 0.274

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

GnomAD4 genome AF: 0.287 AC: 43687 AN: 152136 Hom.: 6644 Cov.: 32 AF XY: 0.283 AC XY: 21062 AN XY: 74390

Gnomad4 AFR AF: 0.369

Gnomad4 AMR AF: 0.213

Gnomad4 ASJ AF: 0.296

Gnomad4 EAS AF: 0.138

Gnomad4 SAS AF: 0.276

Gnomad4 FIN AF: 0.192

Gnomad4 NFE AF: 0.280

Gnomad4 OTH AF: 0.270

Alfa AF: 0.299 Hom.: 1106

Bravo AF: 0.289

Asia WGS AF: 0.221 AC: 772 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.21
Cadd	Benign	20
Dann	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7571323; hg19: chr2-118832568;