chr1-1161907-T-C

Position:

• chr1-1161907-T-C

Variant summary

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

The XR_007065351.1(LOC124903820):​n.1697T>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.88 in 152,214 control chromosomes in the GnomAD database, including 59,412 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 0.88 (59412 hom., cov: 34)
• Consequence: LOC124903820 XR_007065351.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.09

Genes affected

LOC124903820 (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 (NFE) allele frequency at 95% confidence interval = 0.923 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC124903820	XR_007065351.1	n.1697T>C		non_coding_transcript_exon_variant	3/3
LOC124903820	XR_007065350.1	n.2415T>C		non_coding_transcript_exon_variant	2/2

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.880 AC: 133823 AN: 152096 Hom.: 59369 Cov.: 34

Gnomad AFR AF: 0.818

Gnomad AMI AF: 0.990

Gnomad AMR AF: 0.897

Gnomad ASJ AF: 0.908

Gnomad EAS AF: 0.596

Gnomad SAS AF: 0.880

Gnomad FIN AF: 0.900

Gnomad MID AF: 0.934

Gnomad NFE AF: 0.929

Gnomad OTH AF: 0.873

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

GnomAD4 genome AF: 0.880 AC: 133924 AN: 152214 Hom.: 59412 Cov.: 34 AF XY: 0.878 AC XY: 65366 AN XY: 74432

Gnomad4 AFR AF: 0.818

Gnomad4 AMR AF: 0.897

Gnomad4 ASJ AF: 0.908

Gnomad4 EAS AF: 0.597

Gnomad4 SAS AF: 0.880

Gnomad4 FIN AF: 0.900

Gnomad4 NFE AF: 0.929

Gnomad4 OTH AF: 0.873

Alfa AF: 0.893 Hom.: 3383

Bravo AF: 0.874

Asia WGS AF: 0.751 AC: 2611 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.19
DANN	Benign	0.29

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9442384; hg19: chr1-1097287;