rs1913621

Variant names:

• chr2-98745937-T-C
• rs1913621
• XR_007087150.1:n.416-5383T>C

Variant summary

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

The XR_007087150.1(LOC107985922):​n.416-5383T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.324 in 152,042 control chromosomes in the GnomAD database, including 10,297 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 0.32 (10297 hom., cov: 32)
• Consequence: LOC107985922 XR_007087150.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0730
• Publications: 5 publications found

Genes affected

LOC107985922 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.576 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: 0.324 AC: 49220 AN: 151924 Hom.: 10266 Cov.: 32

Gnomad AFR AF: 0.582

Gnomad AMI AF: 0.247

Gnomad AMR AF: 0.331

Gnomad ASJ AF: 0.212

Gnomad EAS AF: 0.345

Gnomad SAS AF: 0.367

Gnomad FIN AF: 0.117

Gnomad MID AF: 0.206

Gnomad NFE AF: 0.201

Gnomad OTH AF: 0.308

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

GnomAD4 genome AF: 0.324 AC: 49309 AN: 152042 Hom.: 10297 Cov.: 32 AF XY: 0.321 AC XY: 23877 AN XY: 74334

African (AFR) AF: 0.582 AC: 24116 AN: 41442

American (AMR) AF: 0.331 AC: 5054 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.212 AC: 736 AN: 3468

East Asian (EAS) AF: 0.345 AC: 1782 AN: 5162

South Asian (SAS) AF: 0.367 AC: 1765 AN: 4808

European-Finnish (FIN) AF: 0.117 AC: 1241 AN: 10600

Middle Eastern (MID) AF: 0.197 AC: 58 AN: 294

European-Non Finnish (NFE) AF: 0.201 AC: 13679 AN: 67968

Other (OTH) AF: 0.309 AC: 653 AN: 2114

Alfa AF: 0.242 Hom.: 21896

Bravo AF: 0.352

Asia WGS AF: 0.367 AC: 1276 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.2
DANN	Benign	0.32
PhyloP100		-0.073

Splicing

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

Other links and lift over

dbSNP: rs1913621; hg19: chr2-99362400;