rs10498690

chr6-18498116-G-A

Variant summary

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

The XR_926549.3(LOC105374955):n.147+1110G>A 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 0.0352 in 152,266 control chromosomes in the GnomAD database, including 105 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 0.035 (105 hom., cov: 33)
• Consequence: LOC105374955 XR_926549.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.276

Genes affected

LOC105374955 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BS1: Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0352 (5357/152266) while in subpopulation NFE AF= 0.0461 (3136/68022). AF 95% confidence interval is 0.0448. There are 105 homozygotes in gnomad4. There are 2602 alleles in male gnomad4 subpopulation. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd at 105 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105374955	XR_926549.3	n.147+1110G>A		intron_variant, non_coding_transcript_variant
LOC105374955	XR_926548.3	n.147+1110G>A		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0352 AC: 5360 AN: 152150 Hom.: 105 Cov.: 33

Gnomad AFR AF: 0.0175

Gnomad AMI AF: 0.0208

Gnomad AMR AF: 0.0436

Gnomad ASJ AF: 0.0424

Gnomad EAS AF: 0.000963

Gnomad SAS AF: 0.0342

Gnomad FIN AF: 0.0380

Gnomad MID AF: 0.0190

Gnomad NFE AF: 0.0461

Gnomad OTH AF: 0.0416

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

GnomAD4 genome AF: 0.0352 AC: 5357 AN: 152266 Hom.: 105 Cov.: 33 AF XY: 0.0350 AC XY: 2602 AN XY: 74444

Gnomad4 AFR AF: 0.0174

Gnomad4 AMR AF: 0.0435

Gnomad4 ASJ AF: 0.0424

Gnomad4 EAS AF: 0.000965

Gnomad4 SAS AF: 0.0342

Gnomad4 FIN AF: 0.0380

Gnomad4 NFE AF: 0.0461

Gnomad4 OTH AF: 0.0412

Alfa AF: 0.0422 Hom.: 50

Bravo AF: 0.0347

Asia WGS AF: 0.0190 AC: 65 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	0.56
Dann	Benign	0.81

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10498690; hg19: chr6-18498347;