rs4598195

chr7-107862996-A-C

Variant summary

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

The XR_927850.3(LOC105375444):n.41-821T>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 0.34 in 152,132 control chromosomes in the GnomAD database, including 9,662 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 0.34 (9662 hom., cov: 32)
• Consequence: LOC105375444 XR_927850.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.192

Genes affected

LOC105375444 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.417 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105375444	XR_927850.3	n.41-821T>G		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.340 AC: 51707 AN: 152012 Hom.: 9658 Cov.: 32

Gnomad AFR AF: 0.183

Gnomad AMI AF: 0.525

Gnomad AMR AF: 0.362

Gnomad ASJ AF: 0.408

Gnomad EAS AF: 0.343

Gnomad SAS AF: 0.289

Gnomad FIN AF: 0.388

Gnomad MID AF: 0.323

Gnomad NFE AF: 0.421

Gnomad OTH AF: 0.343

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

GnomAD4 genome AF: 0.340 AC: 51712 AN: 152132 Hom.: 9662 Cov.: 32 AF XY: 0.339 AC XY: 25202 AN XY: 74378

Gnomad4 AFR AF: 0.182

Gnomad4 AMR AF: 0.362

Gnomad4 ASJ AF: 0.408

Gnomad4 EAS AF: 0.343

Gnomad4 SAS AF: 0.289

Gnomad4 FIN AF: 0.388

Gnomad4 NFE AF: 0.421

Gnomad4 OTH AF: 0.340

Alfa AF: 0.402 Hom.: 27076

Bravo AF: 0.332

Asia WGS AF: 0.328 AC: 1139 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	8.9
Dann	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4598195; hg19: chr7-107503441;