chr1-207320873-C-A

Position:

• chr1-207320873-C-A

Variant summary

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

The XR_007066838.1(LOC107985251):​n.444+813G>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 0.404 in 144,118 control chromosomes in the GnomAD database, including 11,748 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 0.40 (11748 hom., cov: 28)
• Consequence: LOC107985251 XR_007066838.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.406

Genes affected

LOC107985251 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.441 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC107985251	XR_007066838.1	n.444+813G>T		intron_variant, non_coding_transcript_variant
LOC107985251	XR_007066837.1	n.444+813G>T		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.404 AC: 58155 AN: 144056 Hom.: 11738 Cov.: 28

Gnomad AFR AF: 0.320

Gnomad AMI AF: 0.464

Gnomad AMR AF: 0.451

Gnomad ASJ AF: 0.497

Gnomad EAS AF: 0.370

Gnomad SAS AF: 0.389

Gnomad FIN AF: 0.458

Gnomad MID AF: 0.542

Gnomad NFE AF: 0.427

Gnomad OTH AF: 0.452

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

GnomAD4 genome AF: 0.404 AC: 58175 AN: 144118 Hom.: 11748 Cov.: 28 AF XY: 0.404 AC XY: 28371 AN XY: 70142

Gnomad4 AFR AF: 0.320

Gnomad4 AMR AF: 0.450

Gnomad4 ASJ AF: 0.497

Gnomad4 EAS AF: 0.371

Gnomad4 SAS AF: 0.391

Gnomad4 FIN AF: 0.458

Gnomad4 NFE AF: 0.427

Gnomad4 OTH AF: 0.450

Alfa AF: 0.395 Hom.: 1731

Bravo AF: 0.385

Asia WGS AF: 0.332 AC: 1151 AN: 3460

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	4.3
DANN	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6685886; hg19: chr1-207494218;