chr7-150562476-A-G

Position:

• chr7-150562476-A-G

Variant summary

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

The XM_017012936.2(LOC107986860):​c.571+737T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.356 in 152,068 control chromosomes in the GnomAD database, including 10,304 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 0.36 (10304 hom., cov: 32)
• Consequence: LOC107986860 XM_017012936.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.225

Genes affected

LOC107986860 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.65).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.396 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC107986860	XM_017012936.2	c.571+737T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.356 AC: 54052 AN: 151950 Hom.: 10307 Cov.: 32

Gnomad AFR AF: 0.230

Gnomad AMI AF: 0.468

Gnomad AMR AF: 0.405

Gnomad ASJ AF: 0.354

Gnomad EAS AF: 0.380

Gnomad SAS AF: 0.358

Gnomad FIN AF: 0.529

Gnomad MID AF: 0.294

Gnomad NFE AF: 0.391

Gnomad OTH AF: 0.341

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

GnomAD4 genome AF: 0.356 AC: 54063 AN: 152068 Hom.: 10304 Cov.: 32 AF XY: 0.361 AC XY: 26822 AN XY: 74314

Gnomad4 AFR AF: 0.230

Gnomad4 AMR AF: 0.405

Gnomad4 ASJ AF: 0.354

Gnomad4 EAS AF: 0.380

Gnomad4 SAS AF: 0.358

Gnomad4 FIN AF: 0.529

Gnomad4 NFE AF: 0.391

Gnomad4 OTH AF: 0.341

Alfa AF: 0.380 Hom.: 1810

Bravo AF: 0.342

Asia WGS AF: 0.388 AC: 1352 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.65
CADD	Benign	7.4
DANN	Benign	0.93

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12531207; hg19: chr7-150259564;