chr11-7895165-C-A

Position:

• chr11-7895165-C-A

Variant summary

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

The NR_036678.1(LOC283299):​n.353+10438G>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 0.233 in 152,042 control chromosomes in the GnomAD database, including 4,382 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 0.23 (4382 hom., cov: 32)
• Consequence: LOC283299 NR_036678.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.410

Genes affected

LOC283299 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.29 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC283299	NR_036678.1	n.353+10438G>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000527847.5	n.353+10438G>T		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.232 AC: 35311 AN: 151926 Hom.: 4371 Cov.: 32

Gnomad AFR AF: 0.294

Gnomad AMI AF: 0.112

Gnomad AMR AF: 0.235

Gnomad ASJ AF: 0.280

Gnomad EAS AF: 0.138

Gnomad SAS AF: 0.167

Gnomad FIN AF: 0.262

Gnomad MID AF: 0.197

Gnomad NFE AF: 0.201

Gnomad OTH AF: 0.236

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

GnomAD4 genome AF: 0.233 AC: 35361 AN: 152042 Hom.: 4382 Cov.: 32 AF XY: 0.236 AC XY: 17511 AN XY: 74314

Gnomad4 AFR AF: 0.294

Gnomad4 AMR AF: 0.235

Gnomad4 ASJ AF: 0.280

Gnomad4 EAS AF: 0.138

Gnomad4 SAS AF: 0.167

Gnomad4 FIN AF: 0.262

Gnomad4 NFE AF: 0.201

Gnomad4 OTH AF: 0.237

Alfa AF: 0.194 Hom.: 1731

Bravo AF: 0.237

Asia WGS AF: 0.164 AC: 572 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.3
DANN	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1564632; hg19: chr11-7916712;