chr1-207319994-C-T

Position:

• chr1-207319994-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The XR_007066838.1(LOC107985251):​n.444+1692G>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 0.0147 in 152,226 control chromosomes in the GnomAD database, including 21 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 0.015 (21 hom., cov: 31)
• Consequence: LOC107985251 XR_007066838.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.683

Genes affected

LOC107985251 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BS1: Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0147 (2235/152226) while in subpopulation NFE AF= 0.0205 (1397/67992). AF 95% confidence interval is 0.0197. There are 21 homozygotes in gnomad4. There are 1107 alleles in male gnomad4 subpopulation. Median coverage is 31. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 21 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC107985251	XR_007066838.1	n.444+1692G>A		intron_variant, non_coding_transcript_variant
LOC107985251	XR_007066837.1	n.444+1692G>A		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0147 AC: 2233 AN: 152108 Hom.: 21 Cov.: 31

Gnomad AFR AF: 0.00341

Gnomad AMI AF: 0.00987

Gnomad AMR AF: 0.0145

Gnomad ASJ AF: 0.00749

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00249

Gnomad FIN AF: 0.0364

Gnomad MID AF: 0.0222

Gnomad NFE AF: 0.0205

Gnomad OTH AF: 0.0167

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

GnomAD4 genome AF: 0.0147 AC: 2235 AN: 152226 Hom.: 21 Cov.: 31 AF XY: 0.0149 AC XY: 1107 AN XY: 74436

Gnomad4 AFR AF: 0.00340

Gnomad4 AMR AF: 0.0144

Gnomad4 ASJ AF: 0.00749

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00249

Gnomad4 FIN AF: 0.0364

Gnomad4 NFE AF: 0.0205

Gnomad4 OTH AF: 0.0165

Alfa AF: 0.0163 Hom.: 3

Bravo AF: 0.0130

Asia WGS AF: 0.00202 AC: 7 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.16
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: rs34787256; hg19: chr1-207493339;