rs180241

chr7-93920344-T-Cchr7-93920344-T-G

Variant summary

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

The XR_927751.3(LOC105375402):n.380-3824A>G 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 0.792 in 152,184 control chromosomes in the GnomAD database, including 47,879 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 0.79 (47879 hom., cov: 32)
• Consequence: LOC105375402 XR_927751.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.319

Genes affected

LOC105375402 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.882 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105375402	XR_927751.3	n.380-3824A>G		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.792 AC: 120427 AN: 152066 Hom.: 47843 Cov.: 32

Gnomad AFR AF: 0.830

Gnomad AMI AF: 0.786

Gnomad AMR AF: 0.822

Gnomad ASJ AF: 0.798

Gnomad EAS AF: 0.904

Gnomad SAS AF: 0.751

Gnomad FIN AF: 0.790

Gnomad MID AF: 0.810

Gnomad NFE AF: 0.756

Gnomad OTH AF: 0.796

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

GnomAD4 genome AF: 0.792 AC: 120511 AN: 152184 Hom.: 47879 Cov.: 32 AF XY: 0.795 AC XY: 59124 AN XY: 74386

Gnomad4 AFR AF: 0.830

Gnomad4 AMR AF: 0.822

Gnomad4 ASJ AF: 0.798

Gnomad4 EAS AF: 0.903

Gnomad4 SAS AF: 0.752

Gnomad4 FIN AF: 0.790

Gnomad4 NFE AF: 0.756

Gnomad4 OTH AF: 0.791

Alfa AF: 0.763 Hom.: 42313

Bravo AF: 0.797

Asia WGS AF: 0.814 AC: 2831 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	6.9
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: rs180241; hg19: chr7-93549656;