chr1-19005582-A-G

Position:

• chr1-19005582-A-G

Variant summary

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

The XR_001737918.2(LOC105376815):​n.285+1676T>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 0.233 in 151,928 control chromosomes in the GnomAD database, including 6,366 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 0.23 (6366 hom., cov: 32)
• Consequence: LOC105376815 XR_001737918.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.609

Genes affected

LOC105376815 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.497 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105376815	XR_001737918.2	n.285+1676T>C		intron_variant, non_coding_transcript_variant
LOC105376815	XR_001737919.2	n.285+1676T>C		intron_variant, non_coding_transcript_variant
LOC105376815	XR_947015.2	n.552-8523T>C		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.233 AC: 35339 AN: 151808 Hom.: 6359 Cov.: 32

Gnomad AFR AF: 0.503

Gnomad AMI AF: 0.0471

Gnomad AMR AF: 0.164

Gnomad ASJ AF: 0.138

Gnomad EAS AF: 0.277

Gnomad SAS AF: 0.148

Gnomad FIN AF: 0.112

Gnomad MID AF: 0.134

Gnomad NFE AF: 0.114

Gnomad OTH AF: 0.209

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

GnomAD4 genome AF: 0.233 AC: 35380 AN: 151928 Hom.: 6366 Cov.: 32 AF XY: 0.229 AC XY: 17002 AN XY: 74262

Gnomad4 AFR AF: 0.503

Gnomad4 AMR AF: 0.163

Gnomad4 ASJ AF: 0.138

Gnomad4 EAS AF: 0.277

Gnomad4 SAS AF: 0.148

Gnomad4 FIN AF: 0.112

Gnomad4 NFE AF: 0.114

Gnomad4 OTH AF: 0.209

Alfa AF: 0.168 Hom.: 533

Bravo AF: 0.248

Asia WGS AF: 0.227 AC: 790 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.91
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: rs7523455; hg19: chr1-19332076; COSMIC: COSV59930046;