rs2867161

Positions:

• chr7-68172355-C-A
• chr7-68172355-C-T

Variant summary

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

The ENST00000446187.2(ENSG00000226829):​n.465+12435G>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 0.113 in 152,076 control chromosomes in the GnomAD database, including 1,005 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 0.11 (1005 hom., cov: 32)
• Consequence: ENST00000446187.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.60

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.152 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105375341	XR_927643.4	n.508+12435G>T		intron_variant, non_coding_transcript_variant
LOC105375341	XR_927641.1	n.488-509G>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000446187.2	n.465+12435G>T		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.113 AC: 17097 AN: 151958 Hom.: 995 Cov.: 32

Gnomad AFR AF: 0.155

Gnomad AMI AF: 0.209

Gnomad AMR AF: 0.0775

Gnomad ASJ AF: 0.0637

Gnomad EAS AF: 0.0649

Gnomad SAS AF: 0.145

Gnomad FIN AF: 0.117

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.0966

Gnomad OTH AF: 0.108

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

GnomAD4 genome AF: 0.113 AC: 17144 AN: 152076 Hom.: 1005 Cov.: 32 AF XY: 0.114 AC XY: 8481 AN XY: 74346

Gnomad4 AFR AF: 0.155

Gnomad4 AMR AF: 0.0774

Gnomad4 ASJ AF: 0.0637

Gnomad4 EAS AF: 0.0649

Gnomad4 SAS AF: 0.146

Gnomad4 FIN AF: 0.117

Gnomad4 NFE AF: 0.0966

Gnomad4 OTH AF: 0.113

Alfa AF: 0.0917 Hom.: 794

Bravo AF: 0.110

Asia WGS AF: 0.0970 AC: 338 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.014
DANN	Benign	0.37

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2867161; hg19: chr7-67637342;