1-209072514-T-G

Position:

• chr1-209072514-T-G

Variant summary

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

The XR_001738442.2(LOC107985255):​n.495+60240A>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 0.382 in 152,078 control chromosomes in the GnomAD database, including 11,663 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 0.38 (11663 hom., cov: 33)
• Consequence: LOC107985255 XR_001738442.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00400

Genes affected

LOC107985255 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.711 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC107985255	XR_001738442.2	n.495+60240A>C		intron_variant, non_coding_transcript_variant
LOC107985255	XR_001738441.2	n.495+60240A>C		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.382 AC: 58070 AN: 151956 Hom.: 11661 Cov.: 33

Gnomad AFR AF: 0.334

Gnomad AMI AF: 0.412

Gnomad AMR AF: 0.441

Gnomad ASJ AF: 0.304

Gnomad EAS AF: 0.730

Gnomad SAS AF: 0.311

Gnomad FIN AF: 0.453

Gnomad MID AF: 0.278

Gnomad NFE AF: 0.370

Gnomad OTH AF: 0.366

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

GnomAD4 genome AF: 0.382 AC: 58095 AN: 152078 Hom.: 11663 Cov.: 33 AF XY: 0.387 AC XY: 28766 AN XY: 74328

Gnomad4 AFR AF: 0.333

Gnomad4 AMR AF: 0.441

Gnomad4 ASJ AF: 0.304

Gnomad4 EAS AF: 0.731

Gnomad4 SAS AF: 0.310

Gnomad4 FIN AF: 0.453

Gnomad4 NFE AF: 0.370

Gnomad4 OTH AF: 0.371

Alfa AF: 0.372 Hom.: 20919

Bravo AF: 0.384

Asia WGS AF: 0.504 AC: 1753 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	7.2
DANN	Benign	0.84

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10494916; hg19: chr1-209245859;