rs719736

Variant names:

• chr2-184322417-G-A
• rs719736
• ENST00000671393.1:n.295-10377G>A

Variant summary

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

The ENST00000671393.1(ENSG00000286980):​n.295-10377G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.4 in 151,988 control chromosomes in the GnomAD database, including 14,816 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 0.40 (14816 hom., cov: 32)
• Consequence: ENSG00000286980 ENST00000671393.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00800
• Publications: 5 publications found

Genes affected

ENSG00000286980 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.526 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000671393.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000286980	ENST00000671393.1		n.295-10377G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.400 AC: 60796 AN: 151870 Hom.: 14804 Cov.: 32

Gnomad AFR AF: 0.105

Gnomad AMI AF: 0.325

Gnomad AMR AF: 0.536

Gnomad ASJ AF: 0.596

Gnomad EAS AF: 0.466

Gnomad SAS AF: 0.482

Gnomad FIN AF: 0.501

Gnomad MID AF: 0.547

Gnomad NFE AF: 0.513

Gnomad OTH AF: 0.425

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

GnomAD4 genome AF: 0.400 AC: 60806 AN: 151988 Hom.: 14816 Cov.: 32 AF XY: 0.401 AC XY: 29777 AN XY: 74246

African (AFR) AF: 0.105 AC: 4357 AN: 41484

American (AMR) AF: 0.536 AC: 8175 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.596 AC: 2065 AN: 3462

East Asian (EAS) AF: 0.466 AC: 2401 AN: 5150

South Asian (SAS) AF: 0.481 AC: 2316 AN: 4814

European-Finnish (FIN) AF: 0.501 AC: 5286 AN: 10544

Middle Eastern (MID) AF: 0.541 AC: 159 AN: 294

European-Non Finnish (NFE) AF: 0.513 AC: 34842 AN: 67966

Other (OTH) AF: 0.430 AC: 909 AN: 2112

Alfa AF: 0.490 Hom.: 32829

Bravo AF: 0.391

Asia WGS AF: 0.480 AC: 1667 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.1
DANN	Benign	0.61
PhyloP100		0.0080

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: rs719736;

hg19: chr2-185187144;