chr7-150781315-C-T

Position:

• chr7-150781315-C-T

Variant summary

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

The XR_001745423.2(LOC105375566):​n.81-515G>A 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 0.703 in 152,066 control chromosomes in the GnomAD database, including 38,432 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 0.70 (38432 hom., cov: 31)
• Consequence: LOC105375566 XR_001745423.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.500

Genes affected

LOC105375566 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.85 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105375566	XR_001745423.2	n.81-515G>A		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.703 AC: 106796 AN: 151948 Hom.: 38392 Cov.: 31

Gnomad AFR AF: 0.857

Gnomad AMI AF: 0.568

Gnomad AMR AF: 0.696

Gnomad ASJ AF: 0.740

Gnomad EAS AF: 0.624

Gnomad SAS AF: 0.691

Gnomad FIN AF: 0.557

Gnomad MID AF: 0.690

Gnomad NFE AF: 0.639

Gnomad OTH AF: 0.728

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

GnomAD4 genome AF: 0.703 AC: 106896 AN: 152066 Hom.: 38432 Cov.: 31 AF XY: 0.698 AC XY: 51869 AN XY: 74318

Gnomad4 AFR AF: 0.857

Gnomad4 AMR AF: 0.696

Gnomad4 ASJ AF: 0.740

Gnomad4 EAS AF: 0.623

Gnomad4 SAS AF: 0.690

Gnomad4 FIN AF: 0.557

Gnomad4 NFE AF: 0.639

Gnomad4 OTH AF: 0.726

Alfa AF: 0.674 Hom.: 5949

Bravo AF: 0.718

Asia WGS AF: 0.676 AC: 2354 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	3.4
DANN	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6464104; hg19: chr7-150478403;