chr3-61297047-G-T

Variant names:

• chr3-61297047-G-T
• rs7615788
• XR_001740725.2:n.708-12383C>A

Variant summary

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

The XR_940892.3(LOC105377114):​n.822-12383C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.809 in 152,170 control chromosomes in the GnomAD database, including 51,306 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 0.81 (51306 hom., cov: 32)
• Consequence: LOC105377114 XR_940892.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.107

Genes affected

LOC105377114 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.909 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105377114	XR_001740725.2	n.708-12383C>A		intron_variant	Intron 5 of 5
LOC105377114	XR_940892.3	n.822-12383C>A		intron_variant	Intron 6 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.809 AC: 123060 AN: 152052 Hom.: 51276 Cov.: 32

Gnomad AFR AF: 0.593

Gnomad AMI AF: 0.786

Gnomad AMR AF: 0.782

Gnomad ASJ AF: 0.861

Gnomad EAS AF: 0.923

Gnomad SAS AF: 0.844

Gnomad FIN AF: 0.931

Gnomad MID AF: 0.832

Gnomad NFE AF: 0.915

Gnomad OTH AF: 0.811

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

GnomAD4 genome AF: 0.809 AC: 123142 AN: 152170 Hom.: 51306 Cov.: 32 AF XY: 0.810 AC XY: 60297 AN XY: 74418

Gnomad4 AFR AF: 0.593

Gnomad4 AMR AF: 0.782

Gnomad4 ASJ AF: 0.861

Gnomad4 EAS AF: 0.923

Gnomad4 SAS AF: 0.844

Gnomad4 FIN AF: 0.931

Gnomad4 NFE AF: 0.915

Gnomad4 OTH AF: 0.814

Alfa AF: 0.889 Hom.: 23691

Bravo AF: 0.791

Asia WGS AF: 0.852 AC: 2965 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	15
DANN	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7615788; hg19: chr3-61282721;