rs10495514

chr2-3169079-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The XR_001739257.1(LOC107985840):n.1121+16944C>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 0.0238 in 152,300 control chromosomes in the GnomAD database, including 84 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 0.024 (84 hom., cov: 34)
• Consequence: LOC107985840 XR_001739257.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.492

Genes affected

LOC107985840 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BS1: Variant frequency is greater than expected in population eas. gnomad4 allele frequency = 0.0238 (3622/152300) while in subpopulation EAS AF= 0.0498 (258/5182). AF 95% confidence interval is 0.0448. There are 84 homozygotes in gnomad4. There are 2003 alleles in male gnomad4 subpopulation. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd at 84 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC107985840	XR_001739257.1	n.1121+16944C>T		intron_variant, non_coding_transcript_variant
LOC107985840	XR_001739258.2	n.1122-11951C>T		intron_variant, non_coding_transcript_variant
LOC107985840	XR_007086194.1	n.1121+16944C>T		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0238 AC: 3622 AN: 152182 Hom.: 84 Cov.: 34

Gnomad AFR AF: 0.0176

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0197

Gnomad ASJ AF: 0.0251

Gnomad EAS AF: 0.0499

Gnomad SAS AF: 0.0381

Gnomad FIN AF: 0.0857

Gnomad MID AF: 0.00633

Gnomad NFE AF: 0.0164

Gnomad OTH AF: 0.0162

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

GnomAD4 genome AF: 0.0238 AC: 3622 AN: 152300 Hom.: 84 Cov.: 34 AF XY: 0.0269 AC XY: 2003 AN XY: 74462

Gnomad4 AFR AF: 0.0176

Gnomad4 AMR AF: 0.0196

Gnomad4 ASJ AF: 0.0251

Gnomad4 EAS AF: 0.0498

Gnomad4 SAS AF: 0.0380

Gnomad4 FIN AF: 0.0857

Gnomad4 NFE AF: 0.0164

Gnomad4 OTH AF: 0.0161

Alfa AF: 0.0224 Hom.: 8

Bravo AF: 0.0187

Asia WGS AF: 0.0500 AC: 174 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
Cadd	Benign	1.2
Dann	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10495514; hg19: chr2-3172850;