7-31005031-T-G

Position:

• chr7-31005031-T-G

Variant summary

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

The XR_927158.3(LOC105375221):​n.121+1839A>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 0.174 in 152,028 control chromosomes in the GnomAD database, including 2,480 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 0.17 (2480 hom., cov: 32)
• Consequence: LOC105375221 XR_927158.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.796

Genes affected

LOC105375222 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.215 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105375222	XR_001745156.2	n.716+11679T>G		intron_variant, non_coding_transcript_variant
LOC105375221	XR_927158.3	n.121+1839A>C		intron_variant, non_coding_transcript_variant
LOC105375222	XR_001745155.2	n.716+11679T>G		intron_variant, non_coding_transcript_variant
LOC105375222	XR_927160.2	n.716+11679T>G		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.174 AC: 26423 AN: 151910 Hom.: 2474 Cov.: 32

Gnomad AFR AF: 0.218

Gnomad AMI AF: 0.216

Gnomad AMR AF: 0.142

Gnomad ASJ AF: 0.258

Gnomad EAS AF: 0.0443

Gnomad SAS AF: 0.139

Gnomad FIN AF: 0.113

Gnomad MID AF: 0.272

Gnomad NFE AF: 0.170

Gnomad OTH AF: 0.186

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

GnomAD4 genome AF: 0.174 AC: 26448 AN: 152028 Hom.: 2480 Cov.: 32 AF XY: 0.169 AC XY: 12549 AN XY: 74304

Gnomad4 AFR AF: 0.219

Gnomad4 AMR AF: 0.142

Gnomad4 ASJ AF: 0.258

Gnomad4 EAS AF: 0.0444

Gnomad4 SAS AF: 0.136

Gnomad4 FIN AF: 0.113

Gnomad4 NFE AF: 0.170

Gnomad4 OTH AF: 0.185

Alfa AF: 0.170 Hom.: 3286

Bravo AF: 0.179

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	4.5
DANN	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10255835; hg19: chr7-31044646;