rs11584700

chr1-204607855-A-G

Variant summary

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

The ENST00000453895.1(ENSG00000240710):n.117+4704A>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 0.171 in 152,098 control chromosomes in the GnomAD database, including 2,628 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 0.17 (2628 hom., cov: 32)
• Consequence: ENST00000453895.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.949

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.7).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.306 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105371692	XR_007066814.1	n.16780-196A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000453895.1	n.117+4704A>G		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.171 AC: 26011 AN: 151980 Hom.: 2632 Cov.: 32

Gnomad AFR AF: 0.0773

Gnomad AMI AF: 0.241

Gnomad AMR AF: 0.114

Gnomad ASJ AF: 0.179

Gnomad EAS AF: 0.317

Gnomad SAS AF: 0.252

Gnomad FIN AF: 0.223

Gnomad MID AF: 0.177

Gnomad NFE AF: 0.215

Gnomad OTH AF: 0.165

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

GnomAD4 genome AF: 0.171 AC: 26001 AN: 152098 Hom.: 2628 Cov.: 32 AF XY: 0.172 AC XY: 12758 AN XY: 74324

Gnomad4 AFR AF: 0.0772

Gnomad4 AMR AF: 0.114

Gnomad4 ASJ AF: 0.179

Gnomad4 EAS AF: 0.319

Gnomad4 SAS AF: 0.249

Gnomad4 FIN AF: 0.223

Gnomad4 NFE AF: 0.215

Gnomad4 OTH AF: 0.164

Alfa AF: 0.175 Hom.: 474

Bravo AF: 0.156

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.70
Cadd	Benign	3.1
Dann	Benign	0.82

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11584700; hg19: chr1-204576983;