rs3996352

Variant names:

• chr7-130760175-A-G
• rs3996352
• XR_007060527.1:n.178+22185A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_927976.3(LOC105375508):​n.178+22185A>G variant causes a intron 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_927976.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.897
• Publications: 13 publications found

Genes affected

LOC105375508 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.268 AC: 11108 AN: 41434

American (AMR) AF: 0.388 AC: 5932 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.381 AC: 1321 AN: 3464

East Asian (EAS) AF: 0.306 AC: 1579 AN: 5166

South Asian (SAS) AF: 0.386 AC: 1854 AN: 4808

European-Finnish (FIN) AF: 0.449 AC: 4731 AN: 10526

Middle Eastern (MID) AF: 0.374 AC: 110 AN: 294

European-Non Finnish (NFE) AF: 0.487 AC: 33082 AN: 67942

Other (OTH) AF: 0.422 AC: 890 AN: 2108

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.61
CADD	Benign	6.1
DANN	Benign	0.83
PhyloP100		0.90

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs3996352;

hg19: chr7-130444934;