rs3996352

Positions:

• chr7-130760175-A-G

Variant summary

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

The XR_927978.3(LOC105375508):​n.178+22185A>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 0.4 in 151,932 control chromosomes in the GnomAD database, including 12,964 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 0.40 (12964 hom., cov: 31)
• Consequence: LOC105375508 XR_927978.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.897

Genes affected

LOC105375508 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.61).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.483 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105375508	XR_927978.3	n.178+22185A>G		intron_variant, non_coding_transcript_variant
LOC105375508	XR_007060527.1	n.178+22185A>G		intron_variant, non_coding_transcript_variant
LOC105375508	XR_927976.3	n.178+22185A>G		intron_variant, non_coding_transcript_variant
LOC105375508	XR_927977.3	n.178+22185A>G		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.401 AC: 60829 AN: 151814 Hom.: 12958 Cov.: 31

Gnomad AFR AF: 0.268

Gnomad AMI AF: 0.263

Gnomad AMR AF: 0.389

Gnomad ASJ AF: 0.381

Gnomad EAS AF: 0.306

Gnomad SAS AF: 0.384

Gnomad FIN AF: 0.449

Gnomad MID AF: 0.361

Gnomad NFE AF: 0.487

Gnomad OTH AF: 0.421

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

GnomAD4 genome AF: 0.400 AC: 60847 AN: 151932 Hom.: 12964 Cov.: 31 AF XY: 0.397 AC XY: 29478 AN XY: 74242

Gnomad4 AFR AF: 0.268

Gnomad4 AMR AF: 0.388

Gnomad4 ASJ AF: 0.381

Gnomad4 EAS AF: 0.306

Gnomad4 SAS AF: 0.386

Gnomad4 FIN AF: 0.449

Gnomad4 NFE AF: 0.487

Gnomad4 OTH AF: 0.422

Alfa AF: 0.453 Hom.: 1995

Bravo AF: 0.389

Asia WGS AF: 0.380 AC: 1322 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.61
CADD	Benign	6.1
DANN	Benign	0.83

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3996352; hg19: chr7-130444934;