rs1971376

chr8-23671146-A-G

Variant summary

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

The XR_001745842.2(LOC107986930):n.1312+2396A>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 0.277 in 152,102 control chromosomes in the GnomAD database, including 6,005 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 0.28 (6005 hom., cov: 32)
• Consequence: LOC107986930 XR_001745842.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.398

Genes affected

LOC107986930 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.32 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC107986930	XR_001745842.2	n.1312+2396A>G		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.277 AC: 42136 AN: 151986 Hom.: 6003 Cov.: 32

Gnomad AFR AF: 0.278

Gnomad AMI AF: 0.349

Gnomad AMR AF: 0.304

Gnomad ASJ AF: 0.286

Gnomad EAS AF: 0.280

Gnomad SAS AF: 0.333

Gnomad FIN AF: 0.379

Gnomad MID AF: 0.193

Gnomad NFE AF: 0.250

Gnomad OTH AF: 0.274

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

GnomAD4 genome AF: 0.277 AC: 42165 AN: 152102 Hom.: 6005 Cov.: 32 AF XY: 0.286 AC XY: 21232 AN XY: 74348

Gnomad4 AFR AF: 0.277

Gnomad4 AMR AF: 0.304

Gnomad4 ASJ AF: 0.286

Gnomad4 EAS AF: 0.280

Gnomad4 SAS AF: 0.334

Gnomad4 FIN AF: 0.379

Gnomad4 NFE AF: 0.250

Gnomad4 OTH AF: 0.276

Alfa AF: 0.259 Hom.: 1278

Bravo AF: 0.270

Asia WGS AF: 0.326 AC: 1134 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	2.0
Dann	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1971376; hg19: chr8-23528659;