rs4750005

Positions:

• chr10-6127722-T-C

Variant summary

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

The XR_930619.3(LOC101928080):​n.615-1611A>G variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. 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 0.14 (507 hom., cov: 0)
• Consequence: LOC101928080 XR_930619.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.531

Genes affected

LOC101928080 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.66).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.197 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC101928080	XR_930619.3	n.615-1611A>G		intron_variant, non_coding_transcript_variant
LOC101928080	XR_930620.3	n.615-1639A>G		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.136 AC: 9603 AN: 70690 Hom.: 506 Cov.: 0

Gnomad AFR AF: 0.117

Gnomad AMI AF: 0.202

Gnomad AMR AF: 0.153

Gnomad ASJ AF: 0.209

Gnomad EAS AF: 0.0719

Gnomad SAS AF: 0.214

Gnomad FIN AF: 0.118

Gnomad MID AF: 0.276

Gnomad NFE AF: 0.148

Gnomad OTH AF: 0.160

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

GnomAD4 genome AF: 0.136 AC: 9618 AN: 70798 Hom.: 507 Cov.: 0 AF XY: 0.140 AC XY: 4935 AN XY: 35296

Gnomad4 AFR AF: 0.118

Gnomad4 AMR AF: 0.153

Gnomad4 ASJ AF: 0.209

Gnomad4 EAS AF: 0.0726

Gnomad4 SAS AF: 0.213

Gnomad4 FIN AF: 0.118

Gnomad4 NFE AF: 0.148

Gnomad4 OTH AF: 0.159

Alfa AF: 0.478 Hom.: 24635

Bravo AF: 0.426

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.66
CADD	Benign	1.4
DANN	Benign	0.88

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4750005; hg19: chr10-6169685;