rs4455639

chr6-90590227-C-Achr6-90590227-C-Gchr6-90590227-C-T

Variant summary

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

The XR_007059680.1(LOC124901363):n.1163-421C>A 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 0.742 in 152,078 control chromosomes in the GnomAD database, including 42,768 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 (42768 hom., cov: 32)
• Consequence: LOC124901363 XR_007059680.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.656

Genes affected

LOC124901363 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.885 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124901363	XR_007059680.1	n.1163-421C>A		intron_variant, non_coding_transcript_variant
LOC124901363	XR_007059679.1	n.609-421C>A		intron_variant, non_coding_transcript_variant
LOC124901363	XR_007059681.1	n.558-421C>A		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.742 AC: 112755 AN: 151960 Hom.: 42717 Cov.: 32

Gnomad AFR AF: 0.893

Gnomad AMI AF: 0.607

Gnomad AMR AF: 0.655

Gnomad ASJ AF: 0.810

Gnomad EAS AF: 0.477

Gnomad SAS AF: 0.700

Gnomad FIN AF: 0.639

Gnomad MID AF: 0.823

Gnomad NFE AF: 0.706

Gnomad OTH AF: 0.766

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

GnomAD4 genome AF: 0.742 AC: 112869 AN: 152078 Hom.: 42768 Cov.: 32 AF XY: 0.735 AC XY: 54669 AN XY: 74330

Gnomad4 AFR AF: 0.893

Gnomad4 AMR AF: 0.655

Gnomad4 ASJ AF: 0.810

Gnomad4 EAS AF: 0.477

Gnomad4 SAS AF: 0.700

Gnomad4 FIN AF: 0.639

Gnomad4 NFE AF: 0.706

Gnomad4 OTH AF: 0.769

Alfa AF: 0.710 Hom.: 10592

Bravo AF: 0.747

Asia WGS AF: 0.664 AC: 2313 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	0.69
Dann	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4455639; hg19: chr6-91299946; COSMIC: COSV65235346;