1-221100362-G-T

Position:

• chr1-221100362-G-T

Variant summary

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

The XR_001738477.2(LOC101929750):​n.1024-4671G>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 0.886 in 152,196 control chromosomes in the GnomAD database, including 59,989 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 0.89 (59989 hom., cov: 31)
• Consequence: LOC101929750 XR_001738477.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.27

Genes affected

LOC101929750 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.61).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.929 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC101929750	XR_001738477.2	n.1024-4671G>T		intron_variant, non_coding_transcript_variant
LOC101929750	XR_001738478.2	n.733-4353G>T		intron_variant, non_coding_transcript_variant
LOC101929750	XR_001738479.2	n.733-4671G>T		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.886 AC: 134799 AN: 152078 Hom.: 59934 Cov.: 31

Gnomad AFR AF: 0.936

Gnomad AMI AF: 0.865

Gnomad AMR AF: 0.775

Gnomad ASJ AF: 0.916

Gnomad EAS AF: 0.816

Gnomad SAS AF: 0.890

Gnomad FIN AF: 0.874

Gnomad MID AF: 0.892

Gnomad NFE AF: 0.887

Gnomad OTH AF: 0.873

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

GnomAD4 genome AF: 0.886 AC: 134910 AN: 152196 Hom.: 59989 Cov.: 31 AF XY: 0.883 AC XY: 65668 AN XY: 74396

Gnomad4 AFR AF: 0.937

Gnomad4 AMR AF: 0.774

Gnomad4 ASJ AF: 0.916

Gnomad4 EAS AF: 0.817

Gnomad4 SAS AF: 0.890

Gnomad4 FIN AF: 0.874

Gnomad4 NFE AF: 0.887

Gnomad4 OTH AF: 0.873

Alfa AF: 0.871 Hom.: 9834

Bravo AF: 0.876

Asia WGS AF: 0.844 AC: 2934 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.61
CADD	Benign	11
DANN	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6541172; hg19: chr1-221273704;