chr7-150353338-T-C

Position:

• chr7-150353338-T-C

Variant summary

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

The XR_001745420.3(LOC107986858):​n.608-3961T>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 0.228 in 152,078 control chromosomes in the GnomAD database, including 4,291 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 0.23 (4291 hom., cov: 31)
• Consequence: LOC107986858 XR_001745420.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.386

Genes affected

LOC107986858 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.332 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC107986858	XR_001745420.3	n.608-3961T>C		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.228 AC: 34640 AN: 151960 Hom.: 4293 Cov.: 31

Gnomad AFR AF: 0.129

Gnomad AMI AF: 0.405

Gnomad AMR AF: 0.165

Gnomad ASJ AF: 0.311

Gnomad EAS AF: 0.282

Gnomad SAS AF: 0.346

Gnomad FIN AF: 0.279

Gnomad MID AF: 0.256

Gnomad NFE AF: 0.275

Gnomad OTH AF: 0.215

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

GnomAD4 genome AF: 0.228 AC: 34644 AN: 152078 Hom.: 4291 Cov.: 31 AF XY: 0.231 AC XY: 17154 AN XY: 74310

Gnomad4 AFR AF: 0.129

Gnomad4 AMR AF: 0.164

Gnomad4 ASJ AF: 0.311

Gnomad4 EAS AF: 0.282

Gnomad4 SAS AF: 0.346

Gnomad4 FIN AF: 0.279

Gnomad4 NFE AF: 0.276

Gnomad4 OTH AF: 0.212

Alfa AF: 0.266 Hom.: 9042

Bravo AF: 0.212

Asia WGS AF: 0.299 AC: 1042 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	5.9
DANN	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10259796; hg19: chr7-150050427;