11-7874329-G-T

Position:

• chr11-7874329-G-T

Variant summary

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

The NR_036678.1(LOC283299):​n.848+4678C>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 0.0889 in 152,026 control chromosomes in the GnomAD database, including 742 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 0.089 (742 hom., cov: 32)
• Consequence: LOC283299 NR_036678.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.772

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.232 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC283299	NR_036678.1	n.848+4678C>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000529488.5	n.531+4678C>A		intron_variant, non_coding_transcript_variant		5
	ENST00000527847.5	n.848+4678C>A		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.0888 AC: 13490 AN: 151908 Hom.: 741 Cov.: 32

Gnomad AFR AF: 0.120

Gnomad AMI AF: 0.128

Gnomad AMR AF: 0.0728

Gnomad ASJ AF: 0.0744

Gnomad EAS AF: 0.243

Gnomad SAS AF: 0.141

Gnomad FIN AF: 0.0419

Gnomad MID AF: 0.142

Gnomad NFE AF: 0.0649

Gnomad OTH AF: 0.103

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

GnomAD4 genome AF: 0.0889 AC: 13513 AN: 152026 Hom.: 742 Cov.: 32 AF XY: 0.0898 AC XY: 6675 AN XY: 74318

Gnomad4 AFR AF: 0.120

Gnomad4 AMR AF: 0.0727

Gnomad4 ASJ AF: 0.0744

Gnomad4 EAS AF: 0.244

Gnomad4 SAS AF: 0.141

Gnomad4 FIN AF: 0.0419

Gnomad4 NFE AF: 0.0648

Gnomad4 OTH AF: 0.103

Alfa AF: 0.0724 Hom.: 954

Bravo AF: 0.0924

Asia WGS AF: 0.177 AC: 616 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.0
DANN	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10500702; hg19: chr11-7895876;