rs34858744

Positions:

• chr1-207319604-G-C

Variant summary

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

The XR_007066838.1(LOC107985251):​n.444+2082C>G 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 0.0415 in 152,256 control chromosomes in the GnomAD database, including 206 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 0.042 (206 hom., cov: 31)
• Consequence: LOC107985251 XR_007066838.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.441

Genes affected

LOC107985251 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0935 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC107985251	XR_007066838.1	n.444+2082C>G		intron_variant, non_coding_transcript_variant
LOC107985251	XR_007066837.1	n.444+2082C>G		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0415 AC: 6318 AN: 152138 Hom.: 206 Cov.: 31

Gnomad AFR AF: 0.0961

Gnomad AMI AF: 0.00987

Gnomad AMR AF: 0.0256

Gnomad ASJ AF: 0.00749

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00331

Gnomad FIN AF: 0.0365

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.0210

Gnomad OTH AF: 0.0363

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

GnomAD4 genome AF: 0.0415 AC: 6326 AN: 152256 Hom.: 206 Cov.: 31 AF XY: 0.0407 AC XY: 3032 AN XY: 74434

Gnomad4 AFR AF: 0.0960

Gnomad4 AMR AF: 0.0256

Gnomad4 ASJ AF: 0.00749

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00331

Gnomad4 FIN AF: 0.0365

Gnomad4 NFE AF: 0.0210

Gnomad4 OTH AF: 0.0360

Alfa AF: 0.0320 Hom.: 20

Bravo AF: 0.0445

Asia WGS AF: 0.00577 AC: 20 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	8.6
DANN	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs34858744; hg19: chr1-207492949;