chr7-150652849-A-G

Position:

• chr7-150652849-A-G

Variant summary

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

The XR_007060589.1(LOC124901774):​n.285-3958T>C variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.569 in 151,868 control chromosomes in the GnomAD database, including 25,028 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 0.57 (25028 hom., cov: 32)
• Consequence: LOC124901774 XR_007060589.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.992

Genes affected

LOC124901774 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.642 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC124901774	XR_007060589.1	n.285-3958T>C		intron_variant, non_coding_transcript_variant
LOC124901774	XR_007060588.1	n.699-3958T>C		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.569 AC: 86362 AN: 151748 Hom.: 25005 Cov.: 32

Gnomad AFR AF: 0.649

Gnomad AMI AF: 0.513

Gnomad AMR AF: 0.574

Gnomad ASJ AF: 0.506

Gnomad EAS AF: 0.513

Gnomad SAS AF: 0.646

Gnomad FIN AF: 0.621

Gnomad MID AF: 0.509

Gnomad NFE AF: 0.516

Gnomad OTH AF: 0.529

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

GnomAD4 genome AF: 0.569 AC: 86440 AN: 151868 Hom.: 25028 Cov.: 32 AF XY: 0.575 AC XY: 42687 AN XY: 74186

Gnomad4 AFR AF: 0.649

Gnomad4 AMR AF: 0.574

Gnomad4 ASJ AF: 0.506

Gnomad4 EAS AF: 0.513

Gnomad4 SAS AF: 0.645

Gnomad4 FIN AF: 0.621

Gnomad4 NFE AF: 0.516

Gnomad4 OTH AF: 0.531

Alfa AF: 0.520 Hom.: 41358

Bravo AF: 0.568

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	6.2
DANN	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10266069; hg19: chr7-150349937;