rs7542900

chr1-94604485-T-C

Variant summary

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

The XR_001738160.3(LOC105378861):n.512-31306T>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 0.738 in 152,172 control chromosomes in the GnomAD database, including 42,389 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 0.74 (42389 hom., cov: 33)
• Consequence: LOC105378861 XR_001738160.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00300

Genes affected

LOC105378861 (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 = 0.808 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105378861	XR_001738160.3	n.512-31306T>C		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.738 AC: 112251 AN: 152054 Hom.: 42378 Cov.: 33

Gnomad AFR AF: 0.578

Gnomad AMI AF: 0.887

Gnomad AMR AF: 0.719

Gnomad ASJ AF: 0.849

Gnomad EAS AF: 0.679

Gnomad SAS AF: 0.776

Gnomad FIN AF: 0.867

Gnomad MID AF: 0.801

Gnomad NFE AF: 0.814

Gnomad OTH AF: 0.734

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

GnomAD4 genome AF: 0.738 AC: 112308 AN: 152172 Hom.: 42389 Cov.: 33 AF XY: 0.740 AC XY: 55058 AN XY: 74432

Gnomad4 AFR AF: 0.578

Gnomad4 AMR AF: 0.718

Gnomad4 ASJ AF: 0.849

Gnomad4 EAS AF: 0.679

Gnomad4 SAS AF: 0.776

Gnomad4 FIN AF: 0.867

Gnomad4 NFE AF: 0.814

Gnomad4 OTH AF: 0.734

Alfa AF: 0.795 Hom.: 105608

Bravo AF: 0.720

Asia WGS AF: 0.724 AC: 2518 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	4.5
Dann	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7542900; hg19: chr1-95070041; COSMIC: COSV59973914;