rs778430

chr1-56198547-G-Achr1-56198547-G-C

Variant summary

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

The XR_007066111.1(LOC124904190):n.197-1187G>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 0.654 in 152,114 control chromosomes in the GnomAD database, including 33,507 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 0.65 (33507 hom., cov: 32)
• Consequence: LOC124904190 XR_007066111.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.490

Genes affected

LOC124904190 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.804 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124904190	XR_007066111.1	n.197-1187G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000641302.1	n.323-14927C>T		intron_variant, non_coding_transcript_variant
	ENST00000641348.1	n.303-14927C>T		intron_variant, non_coding_transcript_variant
	ENST00000641611.1	n.329-14927C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.654 AC: 99373 AN: 151996 Hom.: 33457 Cov.: 32

Gnomad AFR AF: 0.811

Gnomad AMI AF: 0.515

Gnomad AMR AF: 0.600

Gnomad ASJ AF: 0.695

Gnomad EAS AF: 0.505

Gnomad SAS AF: 0.759

Gnomad FIN AF: 0.516

Gnomad MID AF: 0.766

Gnomad NFE AF: 0.594

Gnomad OTH AF: 0.669

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

GnomAD4 genome AF: 0.654 AC: 99472 AN: 152114 Hom.: 33507 Cov.: 32 AF XY: 0.651 AC XY: 48384 AN XY: 74374

Gnomad4 AFR AF: 0.811

Gnomad4 AMR AF: 0.599

Gnomad4 ASJ AF: 0.695

Gnomad4 EAS AF: 0.504

Gnomad4 SAS AF: 0.760

Gnomad4 FIN AF: 0.516

Gnomad4 NFE AF: 0.595

Gnomad4 OTH AF: 0.671

Alfa AF: 0.628 Hom.: 6454

Bravo AF: 0.662

Asia WGS AF: 0.671 AC: 2335 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
Cadd	Benign	2.6
Dann	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs778430; hg19: chr1-56664219;