rs223930

Variant names:

• chr4-12900411-A-C
• rs223930
• XR_007058045.1:n.2964T>G

Your query was ambiguous. Multiple possible variants found:

• chr4-12900411-A-C
• chr4-12900411-A-G
• chr4-12900411-A-T

Variant summary

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

The XR_007058045.1(LOC105374493):​n.2964T>G 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 0.985 in 152,302 control chromosomes in the GnomAD database, including 73,894 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 0.98 (73894 hom., cov: 32)
• Consequence: LOC105374493 XR_007058045.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.697

Genes affected

LOC105374493 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.993 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105374493	XR_007058045.1	n.2964T>G		non_coding_transcript_exon_variant	Exon 1 of 2
LOC105374493	XR_007058046.1	n.2964T>G		non_coding_transcript_exon_variant	Exon 1 of 2
LOC105374493	XR_001741369.2	n.100-7930T>G		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000302819	ENST00000789800.1	n.121-51718T>G		intron_variant	Intron 1 of 1
ENSG00000302819	ENST00000789804.1	n.371-10405T>G		intron_variant	Intron 1 of 2
ENSG00000302819	ENST00000789805.1	n.371-7930T>G		intron_variant	Intron 1 of 4

Frequencies

GnomAD3 genomes AF: 0.985 AC: 149867 AN: 152184 Hom.: 73837 Cov.: 32

Gnomad AFR AF: 0.947

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.994

Gnomad ASJ AF: 1.00

Gnomad EAS AF: 1.00

Gnomad SAS AF: 1.00

Gnomad FIN AF: 1.00

Gnomad MID AF: 1.00

Gnomad NFE AF: 1.00

Gnomad OTH AF: 0.988

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

GnomAD4 genome AF: 0.985 AC: 149983 AN: 152302 Hom.: 73894 Cov.: 32 AF XY: 0.985 AC XY: 73361 AN XY: 74482

African (AFR) AF: 0.947 AC: 39357 AN: 41544

American (AMR) AF: 0.994 AC: 15216 AN: 15304

Ashkenazi Jewish (ASJ) AF: 1.00 AC: 3472 AN: 3472

East Asian (EAS) AF: 1.00 AC: 5178 AN: 5178

South Asian (SAS) AF: 1.00 AC: 4826 AN: 4828

European-Finnish (FIN) AF: 1.00 AC: 10620 AN: 10620

Middle Eastern (MID) AF: 1.00 AC: 294 AN: 294

European-Non Finnish (NFE) AF: 1.00 AC: 68019 AN: 68036

Other (OTH) AF: 0.988 AC: 2089 AN: 2114

Alfa AF: 0.989 Hom.: 9625

Bravo AF: 0.983

Asia WGS AF: 0.997 AC: 3468 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.54
DANN	Benign	0.54
PhyloP100		-0.70

Splicing

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

Publications

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Other links and lift over

dbSNP: rs223930; hg19: chr4-12902035;