rs11587235

Positions:

• chr1-55835227-G-A

Variant summary

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

The XR_947380.3(LOC105378740):​n.214+19487C>T 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 0.0723 in 152,150 control chromosomes in the GnomAD database, including 468 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 0.072 (468 hom., cov: 33)
• Consequence: LOC105378740 XR_947380.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.642

Genes affected

LOC105378740 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.135 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105378740	XR_947380.3	n.214+19487C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000424357.1	n.257+2802G>A		intron_variant, non_coding_transcript_variant		3
	ENST00000646266.1	n.248+2802G>A		intron_variant, non_coding_transcript_variant
	ENST00000659410.1	n.267+2802G>A		intron_variant, non_coding_transcript_variant
	ENST00000661225.1	n.76+2802G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0722 AC: 10977 AN: 152032 Hom.: 464 Cov.: 33

Gnomad AFR AF: 0.0896

Gnomad AMI AF: 0.0230

Gnomad AMR AF: 0.0420

Gnomad ASJ AF: 0.0323

Gnomad EAS AF: 0.143

Gnomad SAS AF: 0.0296

Gnomad FIN AF: 0.0993

Gnomad MID AF: 0.0127

Gnomad NFE AF: 0.0651

Gnomad OTH AF: 0.0602

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

GnomAD4 genome AF: 0.0723 AC: 11001 AN: 152150 Hom.: 468 Cov.: 33 AF XY: 0.0730 AC XY: 5429 AN XY: 74394

Gnomad4 AFR AF: 0.0899

Gnomad4 AMR AF: 0.0419

Gnomad4 ASJ AF: 0.0323

Gnomad4 EAS AF: 0.143

Gnomad4 SAS AF: 0.0298

Gnomad4 FIN AF: 0.0993

Gnomad4 NFE AF: 0.0651

Gnomad4 OTH AF: 0.0620

Alfa AF: 0.0726 Hom.: 60

Bravo AF: 0.0686

Asia WGS AF: 0.0790 AC: 276 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.66
DANN	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11587235; hg19: chr1-56300900;