11-43875107-T-C

Position:

• chr11-43875107-T-C

Variant summary

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

The ENST00000530450.1(ENSG00000246250):​n.247+2876A>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 0.207 in 152,146 control chromosomes in the GnomAD database, including 3,537 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 (3537 hom., cov: 32)
• Consequence: ENST00000530450.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.202

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.352 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105376644	XR_001748200.2	n.151-178A>G		intron_variant, non_coding_transcript_variant
LOC105376644	XR_931227.3	n.248-178A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000530450.1	n.247+2876A>G		intron_variant, non_coding_transcript_variant		4
	ENST00000528765.1	n.92-178A>G		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.207 AC: 31414 AN: 152028 Hom.: 3535 Cov.: 32

Gnomad AFR AF: 0.137

Gnomad AMI AF: 0.168

Gnomad AMR AF: 0.213

Gnomad ASJ AF: 0.272

Gnomad EAS AF: 0.232

Gnomad SAS AF: 0.367

Gnomad FIN AF: 0.251

Gnomad MID AF: 0.150

Gnomad NFE AF: 0.225

Gnomad OTH AF: 0.210

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

GnomAD4 genome AF: 0.207 AC: 31443 AN: 152146 Hom.: 3537 Cov.: 32 AF XY: 0.210 AC XY: 15603 AN XY: 74372

Gnomad4 AFR AF: 0.137

Gnomad4 AMR AF: 0.214

Gnomad4 ASJ AF: 0.272

Gnomad4 EAS AF: 0.232

Gnomad4 SAS AF: 0.367

Gnomad4 FIN AF: 0.251

Gnomad4 NFE AF: 0.225

Gnomad4 OTH AF: 0.210

Alfa AF: 0.225 Hom.: 2002

Bravo AF: 0.197

Asia WGS AF: 0.277 AC: 964 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	4.9
DANN	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10838192; hg19: chr11-43896657;