chr7-10110349-C-G

Variant names:

• chr7-10110349-C-G
• rs7778619
• XR_001745088.2:n.101-10125G>C

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The XR_001745088.2(LOC105375149):​n.101-10125G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.277 in 151,936 control chromosomes in the GnomAD database, including 10,193 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 (10193 hom., cov: 32)
• Consequence: LOC105375149 XR_001745088.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.11
• Publications: 3 publications found

Genes affected

LOC105375149 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.34).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.648 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105375149	XR_001745088.2	n.101-10125G>C		intron_variant	Intron 1 of 2

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.277 AC: 42056 AN: 151820 Hom.: 10147 Cov.: 32

Gnomad AFR AF: 0.654

Gnomad AMI AF: 0.0318

Gnomad AMR AF: 0.158

Gnomad ASJ AF: 0.119

Gnomad EAS AF: 0.209

Gnomad SAS AF: 0.275

Gnomad FIN AF: 0.190

Gnomad MID AF: 0.242

Gnomad NFE AF: 0.107

Gnomad OTH AF: 0.227

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

GnomAD4 genome AF: 0.277 AC: 42161 AN: 151936 Hom.: 10193 Cov.: 32 AF XY: 0.280 AC XY: 20781 AN XY: 74240

African (AFR) AF: 0.654 AC: 27098 AN: 41420

American (AMR) AF: 0.158 AC: 2413 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.119 AC: 412 AN: 3468

East Asian (EAS) AF: 0.210 AC: 1084 AN: 5154

South Asian (SAS) AF: 0.275 AC: 1324 AN: 4814

European-Finnish (FIN) AF: 0.190 AC: 2008 AN: 10548

Middle Eastern (MID) AF: 0.253 AC: 74 AN: 292

European-Non Finnish (NFE) AF: 0.107 AC: 7240 AN: 67960

Other (OTH) AF: 0.227 AC: 479 AN: 2110

Alfa AF: 0.0675 Hom.: 105

Bravo AF: 0.288

Asia WGS AF: 0.308 AC: 1075 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.34
CADD	Benign	18
DANN	Benign	0.70
PhyloP100		2.1

Splicing

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

Other links and lift over

dbSNP: rs7778619; hg19: chr7-10149976;