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_007060527.1(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_007060527.1 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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105375508	XR_007060527.1	n.178+22185A>G		intron_variant	Intron 3 of 4
LOC105375508	XR_927976.3	n.178+22185A>G		intron_variant	Intron 3 of 5
LOC105375508	XR_927977.3	n.178+22185A>G		intron_variant	Intron 3 of 3
LOC105375508	XR_927978.3	n.178+22185A>G		intron_variant	Intron 3 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

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 v4.3

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

Other links and lift over

dbSNP: rs3996352; hg19: chr7-130444934;