chr1-208935148-G-A

Position:

• chr1-208935148-G-A

Variant summary

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

The XR_001738442.2(LOC107985255):​n.496-112978C>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 0.0979 in 152,174 control chromosomes in the GnomAD database, including 795 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 0.098 (795 hom., cov: 33)
• Consequence: LOC107985255 XR_001738442.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.339

Genes affected

LOC107985255 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.143 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC107985255	XR_001738442.2	n.496-112978C>T		intron_variant, non_coding_transcript_variant
LOC107985255	XR_001738441.2	n.496-112978C>T		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0980 AC: 14908 AN: 152056 Hom.: 798 Cov.: 33

Gnomad AFR AF: 0.0787

Gnomad AMI AF: 0.145

Gnomad AMR AF: 0.0927

Gnomad ASJ AF: 0.156

Gnomad EAS AF: 0.152

Gnomad SAS AF: 0.120

Gnomad FIN AF: 0.0991

Gnomad MID AF: 0.136

Gnomad NFE AF: 0.101

Gnomad OTH AF: 0.110

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

GnomAD4 genome AF: 0.0979 AC: 14905 AN: 152174 Hom.: 795 Cov.: 33 AF XY: 0.0992 AC XY: 7380 AN XY: 74416

Gnomad4 AFR AF: 0.0785

Gnomad4 AMR AF: 0.0925

Gnomad4 ASJ AF: 0.156

Gnomad4 EAS AF: 0.151

Gnomad4 SAS AF: 0.120

Gnomad4 FIN AF: 0.0991

Gnomad4 NFE AF: 0.101

Gnomad4 OTH AF: 0.109

Alfa AF: 0.104 Hom.: 1204

Bravo AF: 0.0965

Asia WGS AF: 0.125 AC: 438 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.60
DANN	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1320539; hg19: chr1-209108493;