rs10498873

Positions:

• chr6-70378113-G-C
• chr6-70378113-G-T

Variant summary

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

The XR_942670.2(LOC105377848):​n.141+3194C>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 0.212 in 151,502 control chromosomes in the GnomAD database, including 4,031 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 0.21 (4031 hom., cov: 29)
• Consequence: LOC105377848 XR_942670.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0790

Genes affected

LOC105377848 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.35 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105377848	XR_942670.2	n.141+3194C>G		intron_variant, non_coding_transcript_variant
LOC105377848	XR_942673.1	n.141+3194C>G		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.212 AC: 32047 AN: 151384 Hom.: 4028 Cov.: 29

Gnomad AFR AF: 0.354

Gnomad AMI AF: 0.0636

Gnomad AMR AF: 0.176

Gnomad ASJ AF: 0.110

Gnomad EAS AF: 0.216

Gnomad SAS AF: 0.235

Gnomad FIN AF: 0.158

Gnomad MID AF: 0.115

Gnomad NFE AF: 0.148

Gnomad OTH AF: 0.178

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

GnomAD4 genome AF: 0.212 AC: 32082 AN: 151502 Hom.: 4031 Cov.: 29 AF XY: 0.212 AC XY: 15673 AN XY: 74030

Gnomad4 AFR AF: 0.354

Gnomad4 AMR AF: 0.176

Gnomad4 ASJ AF: 0.110

Gnomad4 EAS AF: 0.216

Gnomad4 SAS AF: 0.235

Gnomad4 FIN AF: 0.158

Gnomad4 NFE AF: 0.148

Gnomad4 OTH AF: 0.183

Alfa AF: 0.187 Hom.: 368

Bravo AF: 0.216

Asia WGS AF: 0.278 AC: 966 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.7
DANN	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10498873; hg19: chr6-71087816; COSMIC: COSV69404384;