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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107985922	XR_007087150.1	n.416-5383T>C		intron_variant	Intron 1 of 1

Ensembl

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

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 v4.3

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;