rs3758947

Positions:

• chr11-17479663-G-A
• chr11-17479663-G-C

Variant summary

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

The ENST00000662030.1(ENSG00000287898):​n.137+2932G>A 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 0.161 in 152,052 control chromosomes in the GnomAD database, including 2,544 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 0.16 (2544 hom., cov: 32)
• Consequence: ENST00000662030.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.898

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.265 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124902641	XR_007062609.1	n.81+2932G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000662030.1	n.137+2932G>A		intron_variant, non_coding_transcript_variant
	ENST00000666786.1	n.124+2609G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.161 AC: 24438 AN: 151934 Hom.: 2546 Cov.: 32

Gnomad AFR AF: 0.0405

Gnomad AMI AF: 0.172

Gnomad AMR AF: 0.271

Gnomad ASJ AF: 0.141

Gnomad EAS AF: 0.267

Gnomad SAS AF: 0.235

Gnomad FIN AF: 0.245

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.185

Gnomad OTH AF: 0.133

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

GnomAD4 genome AF: 0.161 AC: 24434 AN: 152052 Hom.: 2544 Cov.: 32 AF XY: 0.167 AC XY: 12426 AN XY: 74300

Gnomad4 AFR AF: 0.0404

Gnomad4 AMR AF: 0.272

Gnomad4 ASJ AF: 0.141

Gnomad4 EAS AF: 0.266

Gnomad4 SAS AF: 0.233

Gnomad4 FIN AF: 0.245

Gnomad4 NFE AF: 0.185

Gnomad4 OTH AF: 0.132

Alfa AF: 0.176 Hom.: 3403

Bravo AF: 0.159

Asia WGS AF: 0.237 AC: 824 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	3.1
DANN	Benign	0.80

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3758947; hg19: chr11-17501210;