rs2190321

Variant names:

• chr7-13744186-G-A
• rs2190321
• XR_007060213.1:n.9522G>A

Your query was ambiguous. Multiple possible variants found:

• chr7-13744186-G-A
• chr7-13744186-G-C
• chr7-13744186-G-T

Variant summary

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

The XR_007060213.1(LOC105375161):​n.9522G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.588 in 151,828 control chromosomes in the GnomAD database, including 27,649 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 0.59 (27649 hom., cov: 32)
• Consequence: LOC105375161 XR_007060213.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.705
• Publications: 2 publications found

Genes affected

LOC105375161 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.689 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105375161	XR_007060213.1	n.9522G>A		non_coding_transcript_exon_variant	Exon 4 of 4
LOC105375161	XR_007060216.1	n.8770-6336G>A		intron_variant	Intron 3 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000229618	ENST00000638774.1	n.1161+575G>A		intron_variant	Intron 5 of 6	5
ENSG00000229618	ENST00000791131.1	n.764+575G>A		intron_variant	Intron 6 of 6

Frequencies

GnomAD3 genomes AF: 0.588 AC: 89249 AN: 151710 Hom.: 27650 Cov.: 32

Gnomad AFR AF: 0.401

Gnomad AMI AF: 0.767

Gnomad AMR AF: 0.503

Gnomad ASJ AF: 0.635

Gnomad EAS AF: 0.578

Gnomad SAS AF: 0.592

Gnomad FIN AF: 0.733

Gnomad MID AF: 0.538

Gnomad NFE AF: 0.694

Gnomad OTH AF: 0.593

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

GnomAD4 genome AF: 0.588 AC: 89272 AN: 151828 Hom.: 27649 Cov.: 32 AF XY: 0.584 AC XY: 43315 AN XY: 74220

African (AFR) AF: 0.401 AC: 16601 AN: 41406

American (AMR) AF: 0.503 AC: 7643 AN: 15208

Ashkenazi Jewish (ASJ) AF: 0.635 AC: 2205 AN: 3470

East Asian (EAS) AF: 0.577 AC: 2975 AN: 5154

South Asian (SAS) AF: 0.592 AC: 2854 AN: 4820

European-Finnish (FIN) AF: 0.733 AC: 7747 AN: 10570

Middle Eastern (MID) AF: 0.534 AC: 157 AN: 294

European-Non Finnish (NFE) AF: 0.694 AC: 47142 AN: 67888

Other (OTH) AF: 0.593 AC: 1250 AN: 2108

Alfa AF: 0.611 Hom.: 4830

Bravo AF: 0.567

Asia WGS AF: 0.557 AC: 1939 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	5.6
DANN	Benign	0.62
PhyloP100		0.70

Splicing

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

Other links and lift over

dbSNP: rs2190321; hg19: chr7-13783811;