rs344907

Variant names:

• chr2-139319468-A-C
• rs344907
• ENST00000429008.2:n.146-4455A>C

Your query was ambiguous. Multiple possible variants found:

• chr2-139319468-A-C
• chr2-139319468-A-G
• chr2-139319468-A-T

Variant summary

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

The ENST00000429008.2(ENSG00000226939):​n.146-4455A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.91 in 152,102 control chromosomes in the GnomAD database, including 63,033 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 0.91 (63033 hom., cov: 31)
• Consequence: ENSG00000226939 ENST00000429008.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0820
• Publications: 1 publications found

Genes affected

ENSG00000226939 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.947 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000429008.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LOC105373643	NR_188040.1		n.117-4455A>C		intron	N/A
	LOC105373643	NR_188041.1		n.117-4455A>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000226939	ENST00000429008.2	TSL:4	n.146-4455A>C		intron	N/A
	ENSG00000226939	ENST00000661894.2		n.131-4455A>C		intron	N/A
	ENSG00000226939	ENST00000830494.1		n.176-4455A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.910 AC: 138334 AN: 151984 Hom.: 63006 Cov.: 31

Gnomad AFR AF: 0.880

Gnomad AMI AF: 0.904

Gnomad AMR AF: 0.930

Gnomad ASJ AF: 0.895

Gnomad EAS AF: 0.970

Gnomad SAS AF: 0.897

Gnomad FIN AF: 0.959

Gnomad MID AF: 0.921

Gnomad NFE AF: 0.913

Gnomad OTH AF: 0.918

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

GnomAD4 genome AF: 0.910 AC: 138410 AN: 152102 Hom.: 63033 Cov.: 31 AF XY: 0.912 AC XY: 67794 AN XY: 74338

African (AFR) AF: 0.880 AC: 36490 AN: 41488

American (AMR) AF: 0.930 AC: 14194 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.895 AC: 3109 AN: 3472

East Asian (EAS) AF: 0.970 AC: 4984 AN: 5140

South Asian (SAS) AF: 0.897 AC: 4328 AN: 4826

European-Finnish (FIN) AF: 0.959 AC: 10167 AN: 10600

Middle Eastern (MID) AF: 0.918 AC: 270 AN: 294

European-Non Finnish (NFE) AF: 0.913 AC: 62104 AN: 67990

Other (OTH) AF: 0.919 AC: 1940 AN: 2112

Alfa AF: 0.912 Hom.: 94836

Bravo AF: 0.909

Asia WGS AF: 0.926 AC: 3223 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.4
DANN	Benign	0.49
PhyloP100		-0.082

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs344907;

hg19: chr2-140077038;