chr7-12055340-A-C

Position:

• chr7-12055340-A-C

Variant summary

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

The XR_007060211.1(LOC124901589):​n.85+39313T>G 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 0.121 in 151,942 control chromosomes in the GnomAD database, including 1,304 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 0.12 (1304 hom., cov: 31)
• Consequence: LOC124901589 XR_007060211.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.461

Genes affected

LOC124901589 (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 (NFE) allele frequency at 95% confidence interval = 0.157 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124901589	XR_007060211.1	n.85+39313T>G		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.121 AC: 18398 AN: 151824 Hom.: 1301 Cov.: 31

Gnomad AFR AF: 0.0455

Gnomad AMI AF: 0.228

Gnomad AMR AF: 0.143

Gnomad ASJ AF: 0.194

Gnomad EAS AF: 0.107

Gnomad SAS AF: 0.125

Gnomad FIN AF: 0.106

Gnomad MID AF: 0.193

Gnomad NFE AF: 0.159

Gnomad OTH AF: 0.150

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

GnomAD4 genome AF: 0.121 AC: 18417 AN: 151942 Hom.: 1304 Cov.: 31 AF XY: 0.119 AC XY: 8854 AN XY: 74282

Gnomad4 AFR AF: 0.0457

Gnomad4 AMR AF: 0.144

Gnomad4 ASJ AF: 0.194

Gnomad4 EAS AF: 0.108

Gnomad4 SAS AF: 0.125

Gnomad4 FIN AF: 0.106

Gnomad4 NFE AF: 0.159

Gnomad4 OTH AF: 0.151

Alfa AF: 0.159 Hom.: 4041

Bravo AF: 0.123

Asia WGS AF: 0.123 AC: 428 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	5.3
DANN	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1035147; hg19: chr7-12094966;