rs11242704

chr6-1535763-A-Gchr6-1535763-A-T

Variant summary

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

The XR_427861.4(LOC102723944):n.234+16583T>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 0.424 in 151,848 control chromosomes in the GnomAD database, including 15,936 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 0.42 (15936 hom., cov: 30)
• Consequence: LOC102723944 XR_427861.4 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.402

Genes affected

LOC102723944 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.686 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC102723944	XR_427861.4	n.234+16583T>C		intron_variant, non_coding_transcript_variant
LOC102723944	XR_001743921.2	n.295-6608T>C		intron_variant, non_coding_transcript_variant
LOC102723944	XR_926382.2	n.295-6584T>C		intron_variant, non_coding_transcript_variant
LOC102723944	XR_926384.2	n.260-6584T>C		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.424 AC: 64301 AN: 151730 Hom.: 15907 Cov.: 30

Gnomad AFR AF: 0.693

Gnomad AMI AF: 0.396

Gnomad AMR AF: 0.308

Gnomad ASJ AF: 0.297

Gnomad EAS AF: 0.475

Gnomad SAS AF: 0.372

Gnomad FIN AF: 0.314

Gnomad MID AF: 0.389

Gnomad NFE AF: 0.311

Gnomad OTH AF: 0.392

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

GnomAD4 genome AF: 0.424 AC: 64374 AN: 151848 Hom.: 15936 Cov.: 30 AF XY: 0.421 AC XY: 31248 AN XY: 74208

Gnomad4 AFR AF: 0.693

Gnomad4 AMR AF: 0.308

Gnomad4 ASJ AF: 0.297

Gnomad4 EAS AF: 0.475

Gnomad4 SAS AF: 0.372

Gnomad4 FIN AF: 0.314

Gnomad4 NFE AF: 0.311

Gnomad4 OTH AF: 0.389

Alfa AF: 0.330 Hom.: 10318

Bravo AF: 0.436

Asia WGS AF: 0.417 AC: 1451 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	1.4
Dann	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11242704; hg19: chr6-1535998;