rs10495214

chr1-223684792-T-G

Variant summary

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

The XR_949164.2(LOC105373281):n.340+5980A>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 0.0686 in 152,138 control chromosomes in the GnomAD database, including 775 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 0.069 (775 hom., cov: 32)
• Consequence: LOC105373281 XR_949164.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.985

Genes affected

LOC105373281 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.167 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105373281	XR_949164.2	n.340+5980A>C		intron_variant, non_coding_transcript_variant
LOC105373281	XR_949165.2	n.407+5980A>C		intron_variant, non_coding_transcript_variant
LOC105373281	XR_949166.2	n.96+5980A>C		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0684 AC: 10405 AN: 152020 Hom.: 768 Cov.: 32

Gnomad AFR AF: 0.134

Gnomad AMI AF: 0.0782

Gnomad AMR AF: 0.172

Gnomad ASJ AF: 0.0383

Gnomad EAS AF: 0.167

Gnomad SAS AF: 0.00828

Gnomad FIN AF: 0.0157

Gnomad MID AF: 0.0348

Gnomad NFE AF: 0.0118

Gnomad OTH AF: 0.0731

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

GnomAD4 genome AF: 0.0686 AC: 10435 AN: 152138 Hom.: 775 Cov.: 32 AF XY: 0.0706 AC XY: 5252 AN XY: 74396

Gnomad4 AFR AF: 0.134

Gnomad4 AMR AF: 0.173

Gnomad4 ASJ AF: 0.0383

Gnomad4 EAS AF: 0.167

Gnomad4 SAS AF: 0.00787

Gnomad4 FIN AF: 0.0157

Gnomad4 NFE AF: 0.0118

Gnomad4 OTH AF: 0.0747

Alfa AF: 0.0291 Hom.: 407

Bravo AF: 0.0888

Asia WGS AF: 0.0970 AC: 337 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
Cadd	Benign	0.90
Dann	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10495214; hg19: chr1-223872494;