rs2106595

Variant names:

• chr7-118519495-G-A
• rs2106595
• XR_927909.2:n.426+5668G>A

Variant summary

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

The XR_927909.2(LOC105375473):​n.426+5668G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.259 in 151,250 control chromosomes in the GnomAD database, including 6,120 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 0.26 (6120 hom., cov: 31)
• Consequence: LOC105375473 XR_927909.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.586
• Publications: 10 publications found

Genes affected

LOC105375473 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.345 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105375473	XR_927909.2	n.426+5668G>A		intron_variant	Intron 5 of 9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.260 AC: 39232 AN: 151132 Hom.: 6122 Cov.: 31

Gnomad AFR AF: 0.0952

Gnomad AMI AF: 0.414

Gnomad AMR AF: 0.276

Gnomad ASJ AF: 0.426

Gnomad EAS AF: 0.303

Gnomad SAS AF: 0.211

Gnomad FIN AF: 0.223

Gnomad MID AF: 0.411

Gnomad NFE AF: 0.348

Gnomad OTH AF: 0.313

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

GnomAD4 genome AF: 0.259 AC: 39218 AN: 151250 Hom.: 6120 Cov.: 31 AF XY: 0.254 AC XY: 18743 AN XY: 73862

African (AFR) AF: 0.0949 AC: 3901 AN: 41086

American (AMR) AF: 0.276 AC: 4177 AN: 15156

Ashkenazi Jewish (ASJ) AF: 0.426 AC: 1474 AN: 3458

East Asian (EAS) AF: 0.303 AC: 1545 AN: 5102

South Asian (SAS) AF: 0.210 AC: 1011 AN: 4818

European-Finnish (FIN) AF: 0.223 AC: 2349 AN: 10552

Middle Eastern (MID) AF: 0.415 AC: 122 AN: 294

European-Non Finnish (NFE) AF: 0.348 AC: 23606 AN: 67776

Other (OTH) AF: 0.313 AC: 656 AN: 2098

Alfa AF: 0.220 Hom.: 1234

Bravo AF: 0.261

Asia WGS AF: 0.242 AC: 844 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.7
DANN	Benign	0.56
PhyloP100		-0.59

Splicing

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

Other links and lift over

dbSNP: rs2106595; hg19: chr7-118159549;