7-151025080-A-G

Position:

• chr7-151025080-A-G

Variant summary

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

The XR_007060593.1(LOC124901777):​n.503-47T>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 0.917 in 151,900 control chromosomes in the GnomAD database, including 64,008 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 0.92 (64008 hom., cov: 29)
• Consequence: LOC124901777 XR_007060593.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.25

Genes affected

LOC124901777 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.976 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC124901777	XR_007060593.1	n.503-47T>C		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.917 AC: 139116 AN: 151784 Hom.: 63946 Cov.: 29

Gnomad AFR AF: 0.980

Gnomad AMI AF: 0.896

Gnomad AMR AF: 0.902

Gnomad ASJ AF: 0.873

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.926

Gnomad FIN AF: 0.893

Gnomad MID AF: 0.924

Gnomad NFE AF: 0.881

Gnomad OTH AF: 0.903

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

GnomAD4 genome AF: 0.917 AC: 139236 AN: 151900 Hom.: 64008 Cov.: 29 AF XY: 0.917 AC XY: 68065 AN XY: 74244

Gnomad4 AFR AF: 0.980

Gnomad4 AMR AF: 0.902

Gnomad4 ASJ AF: 0.873

Gnomad4 EAS AF: 0.999

Gnomad4 SAS AF: 0.926

Gnomad4 FIN AF: 0.893

Gnomad4 NFE AF: 0.881

Gnomad4 OTH AF: 0.904

Alfa AF: 0.898 Hom.: 9712

Bravo AF: 0.922

Asia WGS AF: 0.969 AC: 3369 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.29
DANN	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11769158; hg19: chr7-150722167;