rs11771124

chr7-24332751-A-G

Variant summary

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

The ENST00000662001.1(ENSG00000287523):n.71-13266T>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 0.209 in 152,206 control chromosomes in the GnomAD database, including 3,441 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 (3441 hom., cov: 32)
• Consequence: ENST00000662001.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.53

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.239 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC107986777	XR_001745132.2	n.81-13266T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000662001.1	n.71-13266T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.209 AC: 31747 AN: 152088 Hom.: 3442 Cov.: 32

Gnomad AFR AF: 0.198

Gnomad AMI AF: 0.111

Gnomad AMR AF: 0.172

Gnomad ASJ AF: 0.176

Gnomad EAS AF: 0.0997

Gnomad SAS AF: 0.125

Gnomad FIN AF: 0.199

Gnomad MID AF: 0.231

Gnomad NFE AF: 0.242

Gnomad OTH AF: 0.211

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

GnomAD4 genome AF: 0.209 AC: 31757 AN: 152206 Hom.: 3441 Cov.: 32 AF XY: 0.202 AC XY: 15057 AN XY: 74406

Gnomad4 AFR AF: 0.197

Gnomad4 AMR AF: 0.172

Gnomad4 ASJ AF: 0.176

Gnomad4 EAS AF: 0.0996

Gnomad4 SAS AF: 0.125

Gnomad4 FIN AF: 0.199

Gnomad4 NFE AF: 0.242

Gnomad4 OTH AF: 0.213

Alfa AF: 0.224 Hom.: 1116

Bravo AF: 0.209

Asia WGS AF: 0.112 AC: 389 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
Cadd	Benign	0.34
Dann	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11771124; hg19: chr7-24372370;