chr7-130748625-C-T

Variant names:

• chr7-130748625-C-T
• rs4731702
• XR_007060527.1:n.178+10635C>T

Variant summary

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

The XR_927976.3(LOC105375508):​n.178+10635C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.401 in 152,010 control chromosomes in the GnomAD database, including 13,021 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 (13021 hom., cov: 32)
• Consequence: LOC105375508 XR_927976.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.203

Genes affected

LOC105375508 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.484 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105375508	XR_007060527.1	n.178+10635C>T		intron_variant	Intron 3 of 4
LOC105375508	XR_927976.3	n.178+10635C>T		intron_variant	Intron 3 of 5
LOC105375508	XR_927977.3	n.178+10635C>T		intron_variant	Intron 3 of 3
LOC105375508	XR_927978.3	n.178+10635C>T		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: 60954 AN: 151892 Hom.: 13015 Cov.: 32

Gnomad AFR AF: 0.268

Gnomad AMI AF: 0.262

Gnomad AMR AF: 0.389

Gnomad ASJ AF: 0.381

Gnomad EAS AF: 0.307

Gnomad SAS AF: 0.390

Gnomad FIN AF: 0.448

Gnomad MID AF: 0.367

Gnomad NFE AF: 0.488

Gnomad OTH AF: 0.422

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

GnomAD4 genome AF: 0.401 AC: 60973 AN: 152010 Hom.: 13021 Cov.: 32 AF XY: 0.398 AC XY: 29548 AN XY: 74312

Gnomad4 AFR AF: 0.268

Gnomad4 AMR AF: 0.388

Gnomad4 ASJ AF: 0.381

Gnomad4 EAS AF: 0.307

Gnomad4 SAS AF: 0.392

Gnomad4 FIN AF: 0.448

Gnomad4 NFE AF: 0.488

Gnomad4 OTH AF: 0.423

Alfa AF: 0.463 Hom.: 24158

Bravo AF: 0.390

Asia WGS AF: 0.377 AC: 1308 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.87
DANN	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4731702; hg19: chr7-130433384;