rs62421103

Variant names:

• chr6-112839142-G-T
• rs62421103
• XR_001744300.1:n.59+7620C>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_001744300.1(LOC107986634):​n.59+7620C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0429 in 152,142 control chromosomes in the GnomAD database, including 212 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 0.043 (212 hom., cov: 32)
• Consequence: LOC107986634 XR_001744300.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.217
• Publications: 0 publications found

Genes affected

LOC107986634 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0617 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.0430 AC: 6532 AN: 152026 Hom.: 211 Cov.: 32

Gnomad AFR AF: 0.00997

Gnomad AMI AF: 0.0318

Gnomad AMR AF: 0.0319

Gnomad ASJ AF: 0.0332

Gnomad EAS AF: 0.000193

Gnomad SAS AF: 0.00767

Gnomad FIN AF: 0.100

Gnomad MID AF: 0.00633

Gnomad NFE AF: 0.0633

Gnomad OTH AF: 0.0392

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

GnomAD4 genome AF: 0.0429 AC: 6529 AN: 152142 Hom.: 212 Cov.: 32 AF XY: 0.0436 AC XY: 3245 AN XY: 74364

African (AFR) AF: 0.00994 AC: 413 AN: 41538

American (AMR) AF: 0.0318 AC: 486 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.0332 AC: 115 AN: 3464

East Asian (EAS) AF: 0.000194 AC: 1 AN: 5156

South Asian (SAS) AF: 0.00788 AC: 38 AN: 4820

European-Finnish (FIN) AF: 0.100 AC: 1061 AN: 10576

Middle Eastern (MID) AF: 0.00340 AC: 1 AN: 294

European-Non Finnish (NFE) AF: 0.0633 AC: 4303 AN: 67986

Other (OTH) AF: 0.0388 AC: 82 AN: 2112

Alfa AF: 0.0515 Hom.: 93

Bravo AF: 0.0360

Asia WGS AF: 0.00491 AC: 17 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.1
DANN	Benign	0.32
PhyloP100		-0.22

Splicing

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

Other links and lift over

dbSNP: rs62421103; hg19: chr6-113160344;