rs7028041

Positions:

• chr9-108294437-G-A

Variant summary

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

The XR_007061722.1(LOC105376214):​n.720+16229C>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 0.188 in 152,054 control chromosomes in the GnomAD database, including 3,257 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 0.19 (3257 hom., cov: 32)
• Consequence: LOC105376214 XR_007061722.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.135

Genes affected

LOC105376214 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.311 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105376214	XR_007061722.1	n.720+16229C>T		intron_variant, non_coding_transcript_variant
LOC105376214	XR_001746881.2	n.720+16229C>T		intron_variant, non_coding_transcript_variant
LOC105376214	XR_001746882.2	n.720+16229C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.187 AC: 28483 AN: 151936 Hom.: 3243 Cov.: 32

Gnomad AFR AF: 0.316

Gnomad AMI AF: 0.0537

Gnomad AMR AF: 0.179

Gnomad ASJ AF: 0.174

Gnomad EAS AF: 0.0264

Gnomad SAS AF: 0.161

Gnomad FIN AF: 0.145

Gnomad MID AF: 0.146

Gnomad NFE AF: 0.135

Gnomad OTH AF: 0.168

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

GnomAD4 genome AF: 0.188 AC: 28526 AN: 152054 Hom.: 3257 Cov.: 32 AF XY: 0.187 AC XY: 13901 AN XY: 74316

Gnomad4 AFR AF: 0.316

Gnomad4 AMR AF: 0.179

Gnomad4 ASJ AF: 0.174

Gnomad4 EAS AF: 0.0265

Gnomad4 SAS AF: 0.161

Gnomad4 FIN AF: 0.145

Gnomad4 NFE AF: 0.135

Gnomad4 OTH AF: 0.166

Alfa AF: 0.151 Hom.: 893

Bravo AF: 0.189

Asia WGS AF: 0.121 AC: 422 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.2
DANN	Benign	0.29

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7028041; hg19: chr9-111056717;