rs10914967

Positions:

• chr1-34523636-G-A

Variant summary

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

The XR_001737964.2(LOC105378641):​n.577+23943C>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 0.347 in 152,120 control chromosomes in the GnomAD database, including 10,221 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 0.35 (10221 hom., cov: 33)
• Consequence: LOC105378641 XR_001737964.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.389

Genes affected

LOC105378641 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.64).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.507 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105378641	XR_001737964.2	n.577+23943C>T		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.346 AC: 52667 AN: 152002 Hom.: 10209 Cov.: 33

Gnomad AFR AF: 0.513

Gnomad AMI AF: 0.192

Gnomad AMR AF: 0.366

Gnomad ASJ AF: 0.301

Gnomad EAS AF: 0.368

Gnomad SAS AF: 0.483

Gnomad FIN AF: 0.248

Gnomad MID AF: 0.231

Gnomad NFE AF: 0.251

Gnomad OTH AF: 0.318

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

GnomAD4 genome AF: 0.347 AC: 52718 AN: 152120 Hom.: 10221 Cov.: 33 AF XY: 0.351 AC XY: 26063 AN XY: 74354

Gnomad4 AFR AF: 0.512

Gnomad4 AMR AF: 0.367

Gnomad4 ASJ AF: 0.301

Gnomad4 EAS AF: 0.367

Gnomad4 SAS AF: 0.483

Gnomad4 FIN AF: 0.248

Gnomad4 NFE AF: 0.251

Gnomad4 OTH AF: 0.321

Alfa AF: 0.274 Hom.: 5054

Bravo AF: 0.360

Asia WGS AF: 0.460 AC: 1600 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.64
CADD	Benign	14
DANN	Benign	0.89

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10914967; hg19: chr1-34989237;