rs34307182

Positions:

• chr7-33063693-A-C

Variant summary

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

The XR_007060277.1(LOC124901610):​n.464+45A>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 0.304 in 152,130 control chromosomes in the GnomAD database, including 7,375 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 0.30 (7375 hom., cov: 32)
• Consequence: LOC124901610 XR_007060277.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.347

Genes affected

LOC124901610 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.411 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124901610	XR_007060277.1	n.464+45A>C		intron_variant, non_coding_transcript_variant
LOC124901610	XR_007060278.1	n.464+45A>C		intron_variant, non_coding_transcript_variant
LOC124901610	XR_007060279.1	n.464+45A>C		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.304 AC: 46188 AN: 152012 Hom.: 7369 Cov.: 32

Gnomad AFR AF: 0.226

Gnomad AMI AF: 0.305

Gnomad AMR AF: 0.419

Gnomad ASJ AF: 0.296

Gnomad EAS AF: 0.210

Gnomad SAS AF: 0.246

Gnomad FIN AF: 0.347

Gnomad MID AF: 0.313

Gnomad NFE AF: 0.329

Gnomad OTH AF: 0.325

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

GnomAD4 genome AF: 0.304 AC: 46217 AN: 152130 Hom.: 7375 Cov.: 32 AF XY: 0.306 AC XY: 22750 AN XY: 74362

Gnomad4 AFR AF: 0.226

Gnomad4 AMR AF: 0.419

Gnomad4 ASJ AF: 0.296

Gnomad4 EAS AF: 0.210

Gnomad4 SAS AF: 0.248

Gnomad4 FIN AF: 0.347

Gnomad4 NFE AF: 0.329

Gnomad4 OTH AF: 0.321

Alfa AF: 0.307 Hom.: 1050

Bravo AF: 0.307

Asia WGS AF: 0.223 AC: 777 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	3.0
DANN	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs34307182; hg19: chr7-33103305;