rs4075570

Positions:

• chr6-77194092-G-A

Variant summary

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

The XR_241864.5(LOC101928570):​n.1589+17889C>T 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 0.597 in 151,892 control chromosomes in the GnomAD database, including 27,565 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 0.60 (27565 hom., cov: 33)
• Consequence: LOC101928570 XR_241864.5 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0120

Genes affected

LOC101928570 (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 (AMR) allele frequency at 95% confidence interval = 0.652 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC101928570	XR_241864.5	n.1589+17889C>T		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.597 AC: 90605 AN: 151774 Hom.: 27567 Cov.: 33

Gnomad AFR AF: 0.486

Gnomad AMI AF: 0.708

Gnomad AMR AF: 0.663

Gnomad ASJ AF: 0.711

Gnomad EAS AF: 0.617

Gnomad SAS AF: 0.571

Gnomad FIN AF: 0.662

Gnomad MID AF: 0.671

Gnomad NFE AF: 0.631

Gnomad OTH AF: 0.633

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

GnomAD4 genome AF: 0.597 AC: 90652 AN: 151892 Hom.: 27565 Cov.: 33 AF XY: 0.597 AC XY: 44326 AN XY: 74254

Gnomad4 AFR AF: 0.486

Gnomad4 AMR AF: 0.663

Gnomad4 ASJ AF: 0.711

Gnomad4 EAS AF: 0.618

Gnomad4 SAS AF: 0.569

Gnomad4 FIN AF: 0.662

Gnomad4 NFE AF: 0.631

Gnomad4 OTH AF: 0.633

Alfa AF: 0.612 Hom.: 15464

Bravo AF: 0.593

Asia WGS AF: 0.608 AC: 2112 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	0.72
DANN	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4075570; hg19: chr6-77903809;